Chris Jordan has been referred to the Senate's privileges committee over rejecting an upper house order to reveal which companies turning over more than $10 million received JobKeeper payments.

The privileges committee has the power to fine or jail the tax commissioner if he is found in contempt of parliament.

Independent senator Rex Patrick has been campaigning for more transparency around the $90 billion scheme.

The motion to refer Mr Jordan passed the Senate 25 votes to 21 on Tuesday evening.

The ATO boss had refused to release the information because he believed it was not in the public interest to abandon taxpayer confidentiality.

Mr Jordan said he acknowledged and respected the powers of the Senate.

"The Senate Standing Committee of Privileges will now further consider the Senate's order for information about businesses which received JobKeeper," he told the ABC in a statement.

"One of my fundamental roles as commissioner of taxation is to safeguard the integrity of the tax and super systems by ensuring the community's confidence in taxpayer secrecy is maintained."

Senator Patrick and Labor have argued companies that boosted profits pocketed wage subsidies and refused to pay taxpayers back.

Some companies repaid JobKeeper payments after coming under heavy public scrutiny.

Treasurer Josh Frydenberg has railed against calls to release information about JobKeeper receipts, arguing the program overwhelmingly befitted small and medium businesses.

Australian Associated Press