ATO late lodgement penalty: up to $364 per 28 days, capped at $1,820 per document · interest 11.43% p.a. compounding daily · See how to remit them →
The three NDIS-specific issues
1. GST-free does not mean exempt from thinking. Most supports supplied to a participant under a plan are GST-free, but you still register for GST once turnover passes $75,000, still lodge BAS, and still claim input credits on your costs. The two standing errors run in opposite directions: providers charging GST on GST-free supports, which is over-remitting and refundable by revision, and providers assuming GST-free meant no registration or BAS at all, whose backlog is now stacking per-document penalties on statements that were mostly refund positions. That second group is the classic NDIS catch-up, and the ATO frequently owes them money.
2. Worker classification at scale. The sector's workforce is a blend of employees, ABN contractors and people who are honestly both across different engagements. Support work is labour-only by definition, which puts most regular contractor arrangements inside the super net whatever the invoices say. At agency scale that is director-personal super exposure; for the sole trader support worker it is the mirror image - set-aside discipline on the ABN income and a sole trader catch-up if the years got away.
3. Plan-manager and NDIA payment timing. Income recognition across NDIA-managed, plan-managed and self-managed participants lands differently on cash versus accruals. Invoiced-but-unpaid plan-manager claims are the standard reconciliation gap, and getting the timing right period by period in a reconstruction often shrinks what the ATO's estimates assumed. Clean, lodged financials are also what registration audits and platform onboarding increasingly ask for, so the catch-up serves both regulators at once.
The catch-up, NDIS edition
The standard sequence: reconstruct from bank and plan-manager remittance data; lodge BAS oldest-first, which is often a refund position worth collecting; classification and super clean-up where there is a workforce; returns behind; remission on the voluntary disclosure. Growth-stage providers also inherit the structure question mid-catch-up - the sole trader to company move done properly rather than by accident.
Frequently asked questions
Do NDIS providers charge GST?
We never registered for GST because our services are GST-free - is that right?
Are our support workers contractors or employees?
We are two years behind across BAS and returns - how bad is it?
General information only - not personal tax, financial or legal advice. Consider your own circumstances or speak to a registered tax agent. Remission of penalties or interest and payment plans are decisions of the ATO and outcomes can't be guaranteed.