A former Australian Tax Office deputy commissioner who allegedly misused his position to benefit his son has told a Sydney court he was "comfortable and confident" he had done the right thing to avoid a conflict of interest.

Key points: Michael Cranston took the stand in his defence, denying he obtained benefits for his son

Michael Cranston took the stand in his defence, denying he obtained benefits for his son He said he wouldn't have made any decisions about a tax matter involving his son

He said he wouldn't have made any decisions about a tax matter involving his son He said he passed the details onto an assistant commissioner and told him to look into it

Michael Bede Cranston, 59, is accused of influencing his subordinates in an attempt to obtain benefits for his son Adam Cranston, who was connected to the company Plutus Payroll.

The company's accounts had been frozen by the tax office due to alleged unpaid taxes.

Mr Cranston pleaded not guilty to using information he obtained as a deputy commissioner and exercising influence in the capacity of his role, with the intention of dishonestly obtaining a benefit for his son.

On Monday the former deputy commissioner and ATO employee of 40 years began giving evidence at his trial in the NSW District Court.

Mr Cranston told the court his son Adam came to see him in January 2017 and showed him a strongly-worded letter the ATO had sent 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. Son-father things can be taken out of context," he told the court.

"I said, 'I will try to get somebody to deal with it but I cannot get involved in any of the decision-making or any of the detail'."

"I said, 'Leave it with me, I will get somebody senior to look at it'."

Mr Cranston said he then spoke to one of his assistant commissioners, Scott Burrows, and told him to "look into" what area of the ATO this letter had come from.

"I was very concerned about the culture side of it, so I really wanted to know what area," Mr Cranston told the court.

"But I would never have got involved, I would have asked Scott to make the necessary inquiries to the taxpayer's representatives."

When asked if he believed it was a conflict of interest to be raising a tax issue that had been brought to him by his son, Mr Cranston said he did not believe it was.

"The conflict becomes a conflict when you're actually a part of making decisions about the matter," he said.

"I was very comfortable and confident I had done the right thing there."

Mr Cranston will continue giving evidence tomorrow.