The inaugural CEO of the troubled National Disability Insurance Scheme (NDIS) has announced his retirement.

David Bowen has steered the NDIS since 2012, overseeing its three-year trial period and the beginning of its national rollout.

Chairwoman of the agency responsible for the NDIS, Helen Nugent, thanked Mr Bowen for his "excellent stewardship" during its early years.

"Mr Bowen has been instrumental not only in establishing the [agency], but also in ensuring the National Disability Insurance Scheme offers the best possible supports and services to its participants to truly change their lives for the better," Dr Nugent said.

He has also led the NDIS during its problem-plagued transition to full scheme since July last year.

The ABC this week exposed more dramas surrounding the rollout, including provider applications not being processed, training delays for critical staff and properties not being ready.

The latest revelations followed a much-publicised IT meltdown that saw payments to providers frozen and people with disabilities wait weeks for care packages to be approved.

But Dr Nugent said Mr Bowen held a "long-held desire to retire".

He is set to leave in early November.

A long career in the health sector

Before joining the NDIS Mr Bowen was general manager of the NSW Motor Accidents Authority for more than a decade.

Along with helping design the NDIS, he was also one of the architects of the NSW Lifetime Care and Support scheme.

"Mr Bowen has provided outstanding management of the NDIS during its critical early years," Shadow Social Services Minister Jenny Macklin said.

"His knowledge of the insurance industry, health and disability sectors proved invaluable in implementing the NDIS.

"We wish Mr Bowen and his family all the best for the future."

The scheme is expected to cover 460,000 Australians by 2020 and cost $22 billion annually.