In June 2026, the NDIS Quality and Safeguards Commission wrote to 270,000 unregistered NDIS providers putting them on notice. The Commission has named strengthened oversight and regulation of unregistered providers as a regulatory priority. For allied health practice owners — registered or not — the era of light-touch NDIS compliance is over.
This guide covers what the NDIS Commission actually looks for in an audit, the financial cost of non-compliance, and the practical steps to get your practice audit-ready.
What the NDIS Commission Audits
NDIS audits assess compliance with the NDIS Practice Standards and the NDIS Code of Conduct. The key areas for allied health practices are:
- Governance and operational management: Do you have documented policies and procedures? Are they current and accessible to staff?
- Provision of supports: Are supports delivered in accordance with participants’ plans and service agreements? Are progress notes completed within policy timeframes?
- Support planning: Are assessments, goal-setting, and review processes documented?
- Feedback and complaints: Do you have a documented complaints process? Are complaints recorded and acted on?
- Human resources: Are all workers screened? Are qualifications verified? Are supervision arrangements documented?
- Financial management: Are billing practices compliant with NDIS pricing rules? Are service agreements in place for all participants?
The Financial Cost of Non-Compliance
Non-compliance with NDIS requirements carries financial consequences that most practice owners underestimate:
- Payment holds: The NDIS Commission can place a hold on your NDIS payments while an investigation is underway. For a practice generating $50,000/month in NDIS revenue, a 30-day payment hold creates a $50,000 cash flow gap.
- Repayment demands: If the Commission finds billing non-compliance, it can demand repayment of incorrectly claimed amounts. These are treated as income in the year received and repayments are deductible in the year paid — but the cash flow impact is immediate.
- Civil penalties: The Commission can impose civil penalties of up to $187,800 per contravention for registered providers and $37,560 for unregistered providers.
- Banning orders: In serious cases, the Commission can ban individuals from providing NDIS supports. A banning order against a key clinician can destroy the practice’s revenue model.
The Audit Readiness Checklist
Shuriken’s NDIS audit readiness checklist for allied health practices:
- ☐ All workers have current NDIS Worker Screening Checks
- ☐ Service agreements are in place for all current participants
- ☐ Progress notes are completed within 24–48 hours of each session
- ☐ Billing claims match service agreements and progress notes
- ☐ Complaints register is maintained and reviewed quarterly
- ☐ Policies and procedures are documented, current, and accessible
- ☐ Contractor agreements are compliant with ATO and NDIS requirements
- ☐ NF2F and travel billing is compliant with NDIS pricing rules
- ☐ Incident register is maintained for all reportable incidents
- ☐ Staff qualifications and professional registrations are verified and on file
The Tax Treatment of Compliance Costs
NDIS compliance costs are generally tax-deductible as business expenses:
- Audit fees: Verification and certification audit fees are deductible in the year incurred
- Compliance software: Practice management software used for NDIS compliance is deductible (and may qualify for instant asset write-off if it’s a capital item)
- Policy and procedure development: Costs of developing compliance documentation — whether internal labour or external consultants — are deductible
- Worker screening: NDIS Worker Screening Check costs paid by the employer are deductible
The free CARE Assessment includes a Risk & Resilience score that covers NDIS compliance readiness. A low Risk score is the most common finding in practices that have grown quickly without building compliance infrastructure. Take 10 minutes to find out where your practice stands.
See also: Should My Practice Register with the NDIS? | NDIS Pricing 2026-27 Financial Impact
