The lawyer for a former Australian rules footballer accused of financial impropriety has told the Melbourne Magistrates' Court that he believed fraud allegations behind his client's initial arrest could change significantly before the case makes it to trial.

Phil Egan, 60, appeared with his legal team in court reportedly looking quite relaxed on Friday before the case was called for its filing of hearing of the allegations.

He has denied any wrongdoing over the 73 charges between 2010 and 2015 that he stole from a health care organisation for Indigenous communities while in charge.

"I cannot and must not stay silent while my reputation is being attacked by privilege," Mr Egan told The National Indigenous Times before the case was heard.

Mr Egan, who also came to prominence in recent times as the author of a report into alleged systematic racism at Hawthorn Football Club, appeared in court for the first time on Friday since Victoria Police's fraud squad announced the criminal offences.

The charges had related to obtaining financial advantage by deception, using false documents, and receiving secret commissions during the former chief executive's time with the not-for-profit Murray Valley Aboriginal Co-operative in Robinvale.

During the court hearing, lawyers from Doogue and George for Mr Egan, said the case against their client had "significant complexity" with a "number of moving parts".

Richmond's Aboriginal star of the 1980s has been accused of siphoning hundreds of thousands of dollars after police say payments were issued to contractors from the organisation before the money was transferred back into his bank account.

Police started its fraud investigation nearly 12 months ago, but Mr Egan was only first arrested in February before police waited until August 3 before laying charges against the Aberfeldie man.

He has been granted bail on his own undertaking and will return next for a committal mention on October 30.

Mr Egan had been commissioned to investigate whether several First Nations players of Hawthorn had been racially abused while playing at the club.

The allegations were levelled at the club's former coach Alastair Clarkson and football manager Chris Fagan between 2010 and 2016 during their triple premiership reign.

But the AFL cleared the men and no further action is warranted.