It is the second major departure from the agency since Labor's election victory in May, and follows the resignation of NDIA chief executive Martin Hoffman earlier this month.

Dr Napthine declined to comment on why he chose to step away from the role, but he did say he was disappointed.

"I thoroughly enjoyed the opportunity, and my background personally and in my public life has been a lifetime of commitment to people with disabilities and creating choice and opportunities for them... and supporting their carers and families," he said.

"I relished that opportunity and I enjoyed it while I was there but unfortunately it was only a short time."

Dr Napthine, who has his Port Fairy home on the market and is building a new house in Geelong, said he still had plans to relocate in the next 12 months.

That will mean they can be closer to one of three sons, Jack, who has a disability and they fostered as a child.

The agency now faces a leadership vacuum with both positions to be filled by the new government.

In February, the now National Disability Insurance Scheme minister Bill Shorten had labelled then-NDIS minister Linda Reynolds' decision to appoint Dr Napthine a "disgrace" and had urged him not to accept the job.

Dr Napthine officially assumed the role in April, less than two months before the Coalition was ousted.

Mr Shorten acknowledged Dr Napthine's collaboration with the Gillard government as it established the $29.3 billion National Disability Insurance Scheme.

In April, Dr Napthine said it was an honour and privilege to be asked to be board chair.

He and wife Peggy were house parents for the intellectually disabled in Hamilton 40 years ago where they met Jack, and Dr Napthine spent 15 years managing disability housing before entering parliament.

In the late '90s, he was community services minister, which included disability services, and while premier he signed up with then-PM Julia Gillard to establish the NDIS, securing its national headquarters for Geelong.

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