Allan Thomas gave evidence during a committal hearing at the Warrnambool Magistrates Court on Thursday and Wednesday.

Former long-time Framlingham Aboriginal Trust (FAT) administrator Geoff Clark, his wife Trudi and two of their sons, Aaron and Jeremy, have been charged by Victoria Police fraud and extortion squad detectives with a total of 1170 charges after seven-year investigation Operation Omega.

Mr Thomas told the court he was a bookkeeper for FAT between 2001 and 2010 and had lived on properties associated with the trust at Yambuk and Allansford.

The court heard that when Geoff Clark was involved in the national Aboriginal group ATSIC that Jeremy Clark took over as trust chief executive officer.

Mr Thomas said he was asked by Jeremy to transfer funds to legal firm Coadys.

He said many were put through and detailed as legal fees.

In a statement tendered to the court, Mr Thomas said: "I was asked by Trudi Clark and Jeremy Clark not to identify legal fees and I just had to go along with it".

In cross-examination by barrister John Moore, it was put to Mr Thomas that those instructions were never given by Jeremy Clark.

"I do not agree with that at all sir," Mr Thomas replied.

Details of 21 payments were then discussed in the court hearing.

Mr Thomas said he was instructed by Trudi and Jeremy to not accurately record the payments.

"I went back and changed the description from legal fees," he said.

A key component of the police charges relates to legal fees of $900,000 accumulated by Geoff Clark during a series of legal actions during the 2000s.

It's alleged $549,744 was paid to lawyers from FAT and a number of organisations associated with the trust

Under cross-examination by Geoff Clark's barrister Tim Smurthwaite on Thursday morning, Mr Thomas admitted he had been charged with theft from the trust.

It's understood that related to a $10,000 payment in 2008, recorded as a loan, which was not approved by the FAT board.

He pleaded guilty in court during 2018 and was fined.

Mr Thomas denied he committed to give evidence against the Clarks in exchange for police assistance, although he confirmed he told police he would provide a statement for the current case.

He said he was dismissed in 2010 by Geoff Clark without being given a reason and he still didn't know why he was sacked.

The bookkeeper said at that time his theft had not come to light.

Mr Thomas said he was also instructed by Trudi and Jeremy Clark to pay consultancy payments to Geoff Clark even though no consultancy work was provided.

He said Geoff also commanded him to pay him Christmas bonuses.

The bookkeeper also said he was instructed by Trudi and Geoff to continue paying Trudi even when she had finished working for the trust.

He said Geoff also told him to make payments to Coadys solicitors and he recalled payments of $30,000 and $15,000.

Mormon pastor Glen Whautere, who ran Glenn's paintings services which did painting and maintenance work at Framlingham and Brambuk, said he dealt with key prosecution witnesses and former Framlingham employee Michael Fitzgerald.

He said Mr Fitzgerald stuck his nose into other people's business.

In court crown prosecutor Justin Lewis discussed with magistrate Charlie Rozencwajg that Mr Whautere supplied a quote for $83,000 for works that police claim was inflated to $109,000 by Jeremy Clark.

Mr Lewis claimed that about $30,000 flowed back to FAT through Mr Whautere, which was used towards building what was known as Geoff's deck.

He said that deck cost about $100,000 and about half the money came through money from Brambuk, but Geoff did not pay for any of the deck.

Mr Whautere said that Geoff Clark's community vision for the deck was never taken up, possibly due to a tall poppy syndrome, but "it never took off".

The committal hearing continues.

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