Former Australian Tax Office (ATO) deputy commissioner Michael Cranston has been found not guilty of misusing his position to benefit his son.

Mr Cranston was alleged to have set up a meeting between the ATO and payroll company Plutus, which his son was involved with.

The meeting came at a time when the company's accounts were frozen over alleged unpaid taxes and charges of about $40 million.

The court was played an interview between Mr Cranston and Australian Federal Police (AFP) officers on the day he was issued a court attendance notice in May 2017, in which he declared he had “nothing to hide” and only wanted to “help the tax office”.

He told the court his son Adam came to see him after he received a strongly worded letter from the ATO to his business associate Simon Anquetil.

“I was concerned because it's the first time my son raised anything with me to do with taxation and I was grappling with the conflict question,” Mr Cranston said.

“Son-father things can be taken out of context.”

The jury took just over two days to reach its not guilty verdict.