Deputy Australian Tax Office (ATO) commissioner Michael Cranston has resigned after being formally charged in connection with a $130 million fraud.

Mr Cranston is not alleged to have known about the fraud, but is accused of using his position to help his son Adam Cranston, who is being investigated over the matter.

The deputy commissioner was earlier suspended, but has now chosen to resign, effective immediately. He is facing two abuse of power charges.

He is the 11th person to be charged in connection to the alleged syndicate, which is accused of using taxpayers' money to fund lavish lifestyles.

Most of the group were charged on May 17, after a dramatic day of arrests across Sydney.

Michael Cranston was among the nation's most senior public servants, rubbing shoulders with prime ministers as part of his role clamping down on tax avoidance.

The ABC understands he had been employed by the ATO for more than three decades and was involved in the organisation's private groups and high-wealth segment.

Part of his biography on his LinkedIn account reads: "My personal philosophy is that the tax system belongs to all Australians and we all need to work closely together to ensure that it is administered fairly, efficiently and causes the least pain for all that participate."

The AFP has described the investigation as the "most significant" Australian white-collar criminal probe in terms of the number of people and amount of cash involved.

Among the things on their shopping list was 25 motor vehicles, $15 million in bank accounts, 18 residential properties, firearms and two aircrafts.

Michael Cranston was swamped by media as he left the Downing Centre Courts in Sydney. ( AAP: Dean Lewins )

Six of the 11 people charged in relation to the scheme — including Adam and Lauren Cranston — face a maximum of 10 years in prison if found guilty.

The arrests were the result of a joint ATO and Australian Federal Police investigation dating back to June 2016.