Healthcare Operations

A 4-practitioner allied health clinic (physios, occupational therapists, speech pathologists) on Cliniko pays $50–80/practitioner/month. Four practitioners = $200–320/month = $2,400–3,840/year in software licensing alone. Add a second clinic location (4 more practitioners) = $400–640/month ($4,800–7,680/year). Add a third location (4 practitioners) = $600–960/month ($7,200–11,520/year). A 12-practitioner multi-site clinic (3 locations, 4 practitioners each) on Cliniko = $1,200–1,560/month = $14,400–18,720/year. Halaxy is similar pricing ($40–120/seat/month depending on modules). Power Diary costs $60–140/practitioner/month. Now add the gaps: Cliniko doesn't do Medicare Easyclaim (Australian practitioners claim via provider numbers), doesn't integrate NDIS billing (participants claim through approved providers), doesn't auto-draft clinical notes (you're typing notes in Cliniko, then exporting to a separate document management system). Cliniko doesn't host online intake forms (another $100–200/month tool like Typeform or JotForm). Multi-site reporting is fragmented (you're looking at 3 separate Cliniko dashboards, manually consolidating data). The real cost for a 12-practitioner clinic: Cliniko ($14.4k–18.7k), Medicare claiming tool ($200–400/month = $2.4–4.8k/year), NDIS billing module if available ($300–500/month = $3.6–6k/year), intake forms tool ($1.2–2.4k/year), clinical note templates or document management ($100–300/month = $1.2–3.6k/year), multi-site reporting tool or manual Excel consolidation (let's say $50/month = $600/year). Total: $23.4k–39.1k/year in fragmented software. Custom clinic platform — appointments (online + walk-in), Medicare Easyclaim integration, NDIS line-item billing, clinical note templates with RFT/PT/OT compliance, automated intake forms, treatment plans, progress reporting, and multi-site dashboard — costs $50–70k to build. You own it forever. Year one: net cost $50–70k (upfront build). Year two: $600/year hosting + maintenance. Payback: 18–24 months. Year three onwards: you're saving $23–39k annually, and your Medicare claims process is 70% faster, NDIS billing errors drop to near zero, and every practitioner's notes are standardised and auditable.

Why Cliniko & Halaxy Drain Multi-Practitioner Margin

Cliniko's licensing model is straightforward: $50–130/practitioner/month depending on modules. A 4-practitioner clinic pays $200–520/month ($2.4–6.2k/year). Halaxy is $40–120/seat/month (similar math). Power Diary is $60–140/practitioner/month. A 12-practitioner clinic shopping Cliniko at the high end (complex billing module) pays $1,560/month ($18.7k/year). But Cliniko doesn't have built-in Medicare Easyclaim. Most Australian clinics use a third-party claiming service: Easyclaim, HealthOne, or claiming via their practice management system. Those cost $200–400/month ($2.4–4.8k/year) per site. A 3-site clinic: $3 × $300/month = $900/month = $10.8k/year in claiming software. Cliniko also doesn't have NDIS billing natively. If your clinic accepts NDIS participants, you need: an NDIS approval (government regulatory), an NDIS claims module ($300–500/month if available through a third-party), or you're using a separate tool like Careshare, CHC Connect, or a bespoke NDIS billing system ($200–600/month). NDIS participants generate different billing line items (e.g., "2 hours physio at $85/hour", vs "1-hour telehealth assessment at $120"). Standard Cliniko appointment slots don't capture NDIS-specific billing. Clinical notes in Cliniko are free-text (you type in Cliniko's note form). But if your clinic has RFT (Registered Physiotherapist) students or trainees, or you need notes compliance with AHPRA (Australian Health Practitioner Regulation Agency), you might want templated notes. Cliniko has basic templates, but customising them per profession (PT vs OT vs SLP) isn't seamless. Online intake forms in Cliniko exist, but they're limited. Many clinics use Typeform ($25–50/month) or JotForm ($34–99/month) for better UX, then manually transfer intake data to Cliniko. Real cost for a 12-practitioner clinic (3 sites × 4 practitioners):

• Cliniko (3 sites, 4 practitioners each @ $100/mo avg): $14,400/yr
• Medicare claiming tool (Easyclaim or similar): $2,400–4,800/yr
• NDIS billing module or third-party tool: $3,600–7,200/yr
• Online intake forms (Typeform, JotForm): $1,200–2,400/yr
• Clinical note templates or document management: $1,200–3,600/yr
• Multi-site reporting or Excel consolidation (manual labour): ~$600/yr in tools, plus staff time
• Telehealth video platform (Zoom, Whereby, or embedded in Cliniko): $600–2,400/yr
• SMS appointment reminders (if not bundled): $200–600/yr
• Total: ~$24,200–42,000/year

Custom clinic platform: $60–70k upfront build (one-time), $600/year hosting, $3,600/year maintenance (2 hrs/month average updates, bug fixes, compliance audits for AHPRA). Total Year 1: $64.2k. Year 2+: $4.2k/year. Break-even: 18 months. At month 19, you've saved $20k vs Cliniko/Halaxy. Year two: if Cliniko/Halaxy costs $28.2k and custom costs $4.2k, you save $24k. Year three: $24k saved. Year five: $120k saved (minus the $64.2k upfront, you're $55.8k ahead). Multi-site owner with growth plans can't afford Cliniko. At 18 practitioners (4.5 clinics), Cliniko costs $21.6k/year, custom stays at $4.2k/year. You save $17.4k annually on software alone, plus faster Medicare claims (fewer rejections = more cash in), faster NDIS billing (participants reimburse faster = better cash flow), and zero double-entry (intake data flows from form → notes → claims without manual re-entry).

What Custom Replaces: Six Core Modules

1. Online Booking + Walk-In Queue + Telehealth

Client visits clinic website, books 2pm "physio assessment with Sarah" on Wednesday. System checks Sarah's availability (she blocks 1–2pm for admin, so next slot is 2pm). Client books, receives SMS + email confirmation with clinic address and parking info. Wednesday: client walks in at 1:55pm, checks in via iPad in reception. System flags: client pre-booked 2pm with Sarah, Sarah is ready (no waiting). Session starts, Sarah documents in app: "Client reports left knee pain (7/10), ROM limited, positive Lachman test." If clinic offers telehealth, session can switch to video mid-appointment (client on video from home, Sarah in clinic with assessment notes). System records: "2pm physio assessment, in-person 45 min, then telehealth follow-up 15 min = 1 hour total billable." For NDIS participants, system differentiates: "Telehealth assessment" is a different billing line item ($120) vs "in-person physio" ($85/hour). Cliniko does bookings but requires external calendar sync and doesn't differentiate telehealth billing from in-person. Custom system unifies: online booking + walk-in queue + telehealth mode selection + billing line-item rules (in-person vs telehealth vs assessments vs follow-ups).

2. Medicare Easyclaim Integration

Sarah completes assessment: client is referred by GP with a Medicare Enhanced Primary Care (EPC) plan referral (up to 5 physio sessions, 100% covered after 50% gap fee waiver — actually, varies by plan). Sarah enters: patient Medicare number, referring provider details, treatment plan (5 sessions, 2x per week for 2.5 weeks). System auto-calculates: rebate is $49.95 per session (2026 rate), clinic can charge gap fee (usually $20–40 per session). System pre-fills Medicare claiming: patient name, Medicare #, provider number, session date/time, service code (physiotherapy = "52106"), amount claimed, gap fee. At end of week, clinic manager logs into Medicare provider portal (or use Easyclaim API), submits batch of 8 claims. System tracks: 8 claims submitted, 7 approved (1 rejected due to patient eligibility). Total claimed: $7 × $49.95 = $349.65 rebate + $7 × $30 gap = $210 patient gap = $559.65 revenue for 7 sessions. System auto-records: patient owes $210 gap, clinic receives $349.65 rebate. Invoice sent to patient or bulk-billed (if clinic and patient agree). Cliniko doesn't have Easyclaim integration; you're exporting session data, manually entering into Easyclaim portal or asking staff to re-key data in both systems. Custom system integrates: appointment → Medicare claim form auto-populated → direct API submission to Easyclaim → claim status tracked (approved, rejected, pending). Zero manual re-entry.

3. NDIS Billing with Line-Item Reporting

Your clinic is an "approved provider" for NDIS participants. Client books physio session under their NDIS plan. NDIS line items are specific: "Exercise physiology — chronic disease" ($85/hour), "Occupational therapy — group session" ($65/participant/hour, capacity 3), "Speech pathology — 1:1 telehealth" ($90/session). Traditional Cliniko appointment is generic ("Physio Session"). Custom system has NDIS billing modes: appointment type is "NDIS — 1:1 physio", system auto-applies correct line-item code (e.g., "091-041-0134" = Physiotherapy, 1:1, in-person). At end of week, system generates NDIS claim sheet: 4 clients × 5 sessions each = 20 line items, each coded correctly, total $1,700 claimed. Participant (or their support coordinator) reimburses clinic via NDIA portal. System tracks: "NDIS revenue YTD = $34k, 40 participants active, average plan balance per client = $8.5k remaining (3 months left in plan)." For complex NDIS scenarios (dual diagnosis, plan reviews mid-year, support coordination fee structures), custom system templates capture the rules. Cliniko has no NDIS support natively; clinics are using separate NDIS billing tools or spreadsheets. Custom system unifies: NDIS appointment → line-item auto-selected → claim generated → participant reimburses → system tracks plan balance and expiry dates per participant.

4. Clinical Notes with AHPRA-Compliant Templates

After assessment, Sarah writes note. System provides template (RFT — Registered Physiotherapist): Assessment: [client report, ROM, tests, diagnosis] Plan: [goals, frequency, duration, patient education] Treatment: [manual therapy, exercises, modalities] Progress: [response to treatment, compliance, functional gains] Next steps: [discharge plan, referral if needed] Sarah fills: "Assessment: 65M post-op knee replacement (2 weeks), ROM limited 0–80° knee, pain 5/10, walks 100m with frame. Plan: 2x/week physio for 6 weeks, goal ROM 0–110°. Treatment: manual therapy (quad sets, calf stretches), elliptical, walking program. Progress: improving. Next: reassess ROM in 2 weeks." System logs: treatment time (45 min), billing (private: $75; gap from Medicare: $30; NDIS line item: applied if client is NDIS participant). All notes are timestamped, auto-linked to appointments, sortable by client or practitioner. AHPRA compliance: notes are secure (encrypted at rest, audit log shows who accessed when), not deleted (archived if client discharges), and exportable as PDF for client records or GP reports. Cliniko has basic notes, but multi-practitioner compliance (PT notes structured differently from OT notes) requires manual template switching. Custom system: notes are profession-specific, templated, and audit-logged for compliance.

5. Online Intake Forms with Pre-Population

New client visits clinic website, fills intake form: name, DOB, contact, medical history, medications, insurance details (Medicare, private health, NDIS provider number). System auto-saves as draft, SMS link sent: "Complete your intake at [link]." Client completes on phone, form submits. Custom system auto-populates appointment record: client name, DOB, contact phone/email, medical history visible to practitioner at appointment. Practitioner doesn't waste 5 minutes asking "do you have any medical conditions?" — it's already in the chart. NDIS participants: intake form includes "NDIS plan number, plan start/end date, funding allocation, approved provider status." System validates: plan number is checked against NDIA database (if API available), alerts if plan expired. Private health: intake form asks for insurer and policy number, system validates at check-in (some services are private-billed, some are insurance co-claimed). All intake data flows to clinical notes (no re-entry). Cliniko has intake forms, but they're limited in conditional logic (e.g., if client selects "NDIS participant", show NDIS fields; if "Private health", show insurer field). Custom system has smart intake forms: conditional fields, real-time validation, and direct population to appointment/clinical notes without manual transfer.

6. Multi-Site Dashboard + Team Reporting

Clinic manager (or owner of 3-clinic group) opens dashboard. Overview: Site 1 (CBD, 4 practitioners, 85 active clients, $28k YTD revenue), Site 2 (North, 3 practitioners, 62 clients, $22k YTD), Site 3 (West, 2 practitioners, 45 clients, $14k YTD). Total: 9 practitioners, 192 active clients, $64k YTD revenue. Revenue by source: Medicare 32% ($20.5k), Private 28% ($17.9k), NDIS 40% ($25.6k). Practitioner performance: Sarah (PT) is 6 clients/week, $2.8k/month revenue, client satisfaction 9.2/10. Tom (OT) is 4 clients/week, $1.6k/month, satisfaction 8.1/10. Highlight: Tom's client satisfaction dropped from 9.1 to 8.1 last month — drill in: 3 clients discharged (goal-met), 2 clients paused (work conflicts), 1 new referral pending intake. Tom's caseload is healthy but trending down. System suggests: "Referral sources for OT: GP referrals 45%, self-referral 30%, insurance 20%, NDIS 5%. Grow GP referrals via referral lunch-and-learn at local medical clinic." Medicare claims: total $28.5k claimed YTD, $26.2k approved (92% approval rate), $2.3k rejected (coding errors, eligibility). System flags: "4 rejections this month due to patient pre-existing eligibility. Review intake process for eligibility validation." NDIS billing: 45 active participants, average plan balance $8.9k/participant, 40% of plans expire in Q3 (June-Aug). System alerts: "20 participants have 2 months left in current plan. Schedule plan review appointments and update support coordinators." Multi-location reporting: Site 1 is over-booked (5-week waitlist), Site 2 has availability, Site 3 is severely under-utilised. System suggests: "Cross-site referral: refer Site 1 overflow to Site 2 and 3 to balance caseload." Cliniko shows per-site data, but multi-site consolidation is manual (you export 3 CSVs, paste into Excel, create pivot tables). Custom system unifies: one dashboard, 9 practitioners, 3 sites, all KPIs (revenue, claims, satisfaction, waitlist, plan expiry) in one view with alerts and recommendations.

The ROI Math: 12-Practitioner, 3-Site Clinic ($64K Annual Revenue)

Item	Year 1	Year 2+
Custom build (one-time)	$65,000	$0
Hosting (Netlify + Postgres)	$600	$600
Maintenance & updates (2 hrs/mo)	$2,400	$2,400
Total Custom	~$68,000	~$3,000
Cliniko + tools (est.)	$24,200–42,000	$24,200–42,000
Annual Savings (Year 2+)	Loss: $25,800–43,800	Gain: $21,200–39,000

Year one shows upfront build cost, but break-even arrives at month 18–20. Year two, you're $21–39k ahead. Year three, you've saved $42–78k (cumulative). Larger clinics (18 practitioners, 4–5 sites) see the gap widen: Cliniko costs climb to $32k/year, custom stays at $3k/year, saving $29k annually. A growing regional practice that scales from 6 to 12 to 18 practitioners over 3 years bleeds $72k to Cliniko (12 × $6k/year), while custom platform costs stay at $9k total ($68k build + $3k × 1 year). By practitioner scale, custom is non-negotiable above 8 practitioners.

Australian Allied Health Specifics

Medicare rebates for allied health (physio, OT, SLP) are provider-based (practitioner must be registered with Medicare Australia, not the clinic). Referrals come via EPC plan or chronic disease management plan (GP signs off). Rebate rates vary by service (physio = $49.95/session, OT = $58.50/session, SLP = $68.50/session; rates update annually). Claiming requires patient Medicare number, referring provider details, and service code (52106 for physio, 50160 for OT). NDIS billing is plan-based (client has approved provider status, plan manager approves spending, participants claim via My NDIS portal). Line-item codes are granular: physio 1:1 is different from physio group; telehealth is different from in-person; assessments are different from ongoing. Private health insurance rebates vary by policy and insurer (Bupa, HBF, Medibank); system must know per-insurer rebate schedules and validate client eligibility at check-in. AHPRA (Australian Health Practitioner Regulation Agency) requires: practitioner registration numbers linked to appointments (each provider number can claim specific service codes), clinical notes stored securely, and audit trail of who accessed what data (mandatory for privacy breach investigation). Workcover (workplace injury) claims require specific coding and support-worker coordination. GST applies to most services (10% inclusive). Cliniko doesn't have native Medicare Easyclaim, NDIS line-item support, or multi-insurer rebate validation; you're manually integrating. Custom systems embed all of these natively: Medicare rates baked in, NDIS line-item auto-selection per appointment type, private health insurer rebate schedules updatable, AHPRA-compliant audit logging, and GST auto-calculated per transaction.

Six FAQs

What if we're a small clinic (2 practitioners) — is custom platform overkill?

Yes. At 2 practitioners, Cliniko at $100–130/month ($1.2–1.56k/year) is reasonable. Custom platform ($65k upfront) doesn't break even for 4–5 years. Stay on Cliniko until you hit 6–8 practitioners or add a second location. Then custom makes financial sense.

Can we migrate our existing client data and clinical notes from Cliniko to custom?

Yes. Cliniko exports client contact data (name, DOB, phone, email, medical history) as CSV. Custom system imports in hours — 500+ clients restored, no re-entry. Clinical notes are text-based; you can export note history (date, practitioner, content) as JSON and restore to custom system's note archive. Appointments are exported as date/time/service/practitioner and imported as historical records (not re-bookable, but visible for continuity of care).

How do we handle mixed billing (Medicare + Private + NDIS for one client)?

System tracks client's active plans: "Medicare (EPC plan, 3 sessions remaining)", "NDIS ($18k remaining, expires Aug 2026)", "Private health (Bupa policy)." At appointment booking, clinic admin selects which plan to bill against. System auto-applies correct billing code and rebate. One client might have "Session 1 (Medicare, $49.95 rebate)", "Session 2 (NDIS, $85 line item)", "Session 3 (Private, Bupa $58 rebate + $20 gap)." All tracked separately, all claims generated correctly.

What if a Medicare claim is rejected — how do we handle appeals?

System logs rejection reason (e.g., "patient not eligible for EPC plan at time of service"). Manager can review, correct (if it's a data error), and re-submit. If it's a legitimate patient eligibility issue, system flags: "5 rejections this month. Review intake process or educate staff on eligibility validation." Appeals to Medicare are handled via Medicare provider portal (not custom system), but system tracks: "Appealed claim XYZ — status pending (14 days)."

Can we set up templates for different practitioners (PT vs OT vs SLP)?

Yes. System has profession-specific note templates. When Sarah (PT) logs in, her appointments auto-apply PT template (ROM, manual therapy, exercises, functional gains). When Tom (OT) logs in, his template focuses on ADL (activities of daily living), home safety, adaptive equipment. When Priya (SLP) logs in, her template tracks swallow function, speech clarity, communication goals. Templates are customizable per clinic and per practitioner (senior PT might have a more detailed template than junior PT).

How do we handle waitlists and referral tracking?

System tracks referrals: GP sends referral, admin logs it in system ("GP: Dr. Smith, referral date: 2026-06-01, service: physio, reason: post-op knee, EPC plan attached"). System generates waitlist by service type and practitioner availability. Client is offered: "Sarah has 3-week wait, Tom has 1-week wait." System auto-sends reminder emails to referral sources: "You sent 12 referrals in Q2. 10 became appointments, 2 are still on waitlist (4+ weeks). Follow up?" Referral source performance is tracked, helping clinics identify high-volume vs low-conversion referrers.

The Bottom Line

Cliniko and Halaxy are industry defaults because they're quick to set up for a small clinic. But a 12-practitioner multi-site clinic bleeding $24–42k/year on fragmented software (Cliniko + Easyclaim + NDIS tool + intake forms + note management) doesn't need more licensing. It needs one system: appointments unified (online + walk-in + telehealth), Medicare claims auto-generated with zero manual re-entry, NDIS billing with line-item auto-coding, clinical notes templated per profession and AHPRA-compliant, intake forms smart-populated, and multi-site reporting with actionable insights. Custom platform costs $65k upfront, $3k/year to run. Cliniko/Halaxy costs $24–42k/year, forever. Year two, custom is $21–39k ahead. Year five, you've saved $105–195k and own your data, your claims process, your NDIS billing logic, and your competitive advantage. No transaction fees, no per-practitioner licensing, no tool fragmentation. You control the system. You control the client experience. You control the economics.

Ready to build a clinic platform that scales with your practitioners and sites? Check Aidxn's custom software packages, or book a call to map your practitioner count, current pain points, billing mix (Medicare/NDIS/Private), and multi-site ROI timeline.