Jeffrey Chan was suspended in November following a report by ABC's Four Corners, which revealed Irabina remained a service provider with the NDIS for around four years after serious concerns were raised about its practices.
He filed an injunction with the Federal Court to end his suspension, an appeal granted by Justice Yaseen Shariff with reasons published on Friday.
Dr Chan filled a role as national senior practitioner in the newly established NDIS Quality and Safeguards Commission between May and June of 2022, giving him at least some oversight of the teams responsible for managing Irabina.
From around 2019, serious concerns had already been identified with Irabina's practices, including the use of unauthorised restraints and other techniques for managing vulnerable people.
On August 30, 2022 Dr Chan received an email informing him an audit had identified "significant areas of concern" in the services Irabina provided.
"Why any of this was only occurring in 30 August 2022, when Irabina had been 'on the radar' since 2019 was unexplained," Justice Shariff said in his judgment.
"It appears that notwithstanding serious concerns had been raised about Irabina, it continued to provide services as an NDIS provider."
The episode of Four Corners which aired in September this year looked into exploitation, abuse and assault of persons with disabilities by various providers.
NDIS Quality and Safeguards Commissioner Tracy Mackey told the show Irabina's services under the NDIS had been shut down.
Soon after the interview aired, Dr Chan informed Ms Mackey that Irabina had not in fact been shut down, meaning she had unwittingly misled the public.
NDIS commission chief operating officer Lisa Pulko later decided to suspend Dr Chan from working, at least while an independent review into Irabina took place.
Dr Chan was the only person to be suspended over Irabina's conduct despite him only having had limited responsibility for oversight over a few months.
His lawyers argued he had been "thrown under the bus" and made a public "scapegoat".
Dr Chan also gave evidence his reputation was being tarnished by the suspension and that he had suffered serious mental health impacts as a result.
His barrister Dilan Mahendra argued Ms Pulko and others had breached their power in suspending him and in doing so might have engaged in unlawful adverse action against him.
Justice Shariff overruled Dr Chan's suspension on the condition he work from home and provide a report by a mental health practitioner clearing him to perform his duties.
The parties have also been ordered to undergo mediation at the expense of the NDIS commission.
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