A former ATO boss has been accused of misusing his position to benefit his son.

former Australian Tax Office deputy commissioner Michael Cranston has appeared in a Sydney court on allegations he attempted to set up a meeting between the ATO and payroll company Plutus.

Plutus handled pay and superannuation for government departments and businesses, but faced a bill of up to $40 million in taxes and other charges.

Prosecutors say Mr Cranston exerted influence on the audit team handling the Plutus matter, following a request for assistance from his son, who was associated with Plutus.

An ATO investigator who was part of the secret audit of Plutus said she received a letter inquiring about the case that “brought a number of concerns”.

Mr Cranston's lawyer argued that as the letter containing the Plutus tax assessment had Mr Cranston's electronic signature on it, and so he had the right to enquire.

Soon after, the ATO obtained a garnishee order that froze a Plutus bank account and prevented it from conducting business.

Mr Staehli said unpaid contractors talked to the media.

“There was significant publicity at the time, there were a whole lot of contractors who hadn't been paid,” he said.

Mr Cranston tried to organise a meeting between ATO officials and Plutus.

“[Mr Cranston] was trying to make sure the tax office didn't get this type of publicity, where it was seen to have misused its powers,” the lawyer said.

The Crown alleged Adam Cranston asked his father whether the ATO was auditing a business associate named Simon Anquetil.

Peter Neil SC alleged Mr Cranston instructed a subordinate to search confidential tax office records, but found it had been “restricted”.

Mr Neil said Mr Cranston found out enough for his son to “tip off” Mr Anquetil.

“[He had a] clear conflict of interest as a deputy commissioner of taxation who was involved in investigating major suspected tax abusers threatening large amounts of money … some may in fact be criminal at a high level,” he said.

“He should have recused himself immediately and denied the request.”

The trial continues.