The National Disability Insurance Scheme is failing a third of participants, a Flinders University report has found, with intellectually disabled people missing out on services.

An evaluation of the NDIS by Flinders University researchers showed the system worked well for the majority of participants, but about one-third of people felt no better off, and 10 to 20 per cent felt "worse off".

At the same time, a Queensland Audit Office report on the implementation of the NDIS in that state found that while the scheme had benefits, participants reported that the pathway and processes to obtain approved support packages are “frustrating and confusing”. 

The Queensland report found it was “critically important” for state and federal governments to manage the transition to the new model well and work together to ensure that people with a disability have a positive experience connecting to the new scheme.

It also identified uncertainty surrounded services creating potential for gaps: “The lack of certainty over who is responsible for the services increases the risk of poorer service delivery experiences for clients. It also increases the potential for duplication of service systems, and gaps in service.

Disability advocates are concerned about the number of people feeling unhappy with the scheme. 

The Flinders study found the NDIS worked best for participants and families who could "strongly advocate for themselves", and left people with intellectual and psychosocial disabilities as well as older carers with health issues, at a disadvantage.

“This study confirms what we’ve known for some time, that people with mental health issues are falling through the gaps in the scheme,” said Wellways CEO Elizabeth Crowther.

The recent Budget announcement of $9 million for “continuity of support” should help remedy the situation, Ms Crowther said. “But we are concerned vulnerable people are still going to miss out.”

“The NDIS doubles funding for disability support across Australia. They should be feeling as if they're getting much better access to services," National Disability Services chief executive Ken Baker said. 

“It is very concerning that some people with disability feel worse off as a result of the NDIS. The NDIS is founded on great principles, but translating those principles into practice has proved challenging.

“Too many people who are in the NDIS find the system confusing, there is too much paperwork, and many not-for-profit disability organisations are struggling to provide NDIS services and remain financially viable.

Dr Baker said the federal government needed to fix implementation problems with the scheme, including improving the quality of NDIS plans and processes and ensuring that the disability service sector is sustainable and is able to invest in growth to meet the need for services.

“However, disability service organisations will not invest in growth unless they are confident that the fundamentals of the scheme are working well – including that NDIS pricing is right – and that is not the case at present,” said Dr Baker.

“None of these problems is unsolvable. The NDIS has the potential to be a world-leading system. The disability sector is ready to work with government to get it right.”

But Social Services Minister Dan Tehan said "hundreds of staff" were being "added" at the National Disability Insurance Agency, the organisation that implements the NDIS.

As well, a $64 million allocation in the budget across three years to establish an NDIS Jobs and Market Fund would assist the sector.

"As the program ramps up, so too do we have to ramp up the staffing levels," he said. The NDIS is designed to support about 460,000 Australians with disability by 2019 with an annual cost of $22 billion.