The Human Rights Law Centre's Whistleblower Project will urge the federal government to enact stronger protections for people calling out misconduct within the scheme.
The project is Australia's first dedicated legal service for whistleblowers.
A parliamentary inquiry into integrity of the NDIS will be told on Thursday that laws governing the scheme should be amended for eligible whistleblowers to make a disclosure to a lawyer, medical practitioner, union or independent advocate for help with unveiling wrongdoing.
Government-funded legal support should be set up for whistleblowers to report reprisal from their employers and other for speaking out, the centre says.
Madeleine Howle, a Whistleblower Project lawyer, said it was essential that regulators and the public were informed of abuse and neglect of people with disability, in addition to other forms of misconduct.
"We commend the Albanese government's earlier reforms to NDIS whistleblower protections in March, which addressed some of the most glaring issues that were preventing whistleblowers from speaking up," she said.
"But NDIS protections remain piecemeal and out of date. That silences the voices of workers, people with disability and advocates."
Disability Advocacy Network Australia said a complaints system remained "core" to integrity.
"They are a critical path for people with disability to be able to safely raise issues and seek accountability," the submission reads.
"The effectiveness of the system in detecting, preventing and responding to wrongdoing depends in part on people with disability and their supporters continuing to raise complaints."
National Disability Services, Australia's peak industry body, has called for mandatory registration of all providers to make the scheme more accountable.
About 94 per cent of NDIS providers are unregistered, and most are able to operate outside consistent regulatory oversight.
The federal government is overhauling the $50 billion scheme in a bid to claw back tens of billions of dollars in savings to stop the NDIS from growing at an "unsustainable" pace.
This includes a crackdown on fraud and dodgy providers.
The Australian Federal Police, Australian Taxation Office and Australian Transaction Reports and Analysis Centre are among the organisations that will also appear at the inquiry's public hearing.
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