Malcolm Turnbull ordered a top bureaucrat to investigate whether Barnaby Joyce breached ministerial standards, but the probe was dropped when the former Deputy PM quit, it has been revealed.

Finance Minister Mathias Cormann confirmed Mr Turnbull made the request of head of the Department of Prime Minister and Cabinet (DPMC) Martin Parkinson on February 21, less than a week after he slammed Mr Joyce’s conduct in a press conference and banned sex between ministers and their staff.

At a Senate Estimates hearing on Monday, Senator Cormann read out a letter from Dr Parkinson to the Prime Minister that confirmed the inquiry had been dropped because Mr Joyce had quit the ministry.

Dr Parkinson also revealed in the letter, sent on Monday, that the Independent Parliamentary Expenses Authority is conducting an audit into Mr Joyce’s use of his travel entitlements. That review is ongoing.

“In light of Mr Joyce’s decision to step down from the Ministry, I have concluded that there is little to be gained from continuing this investigation,” Dr Parkinson’s letter to the PM said, according to Senator Cormann.

On February 17, at a press conference where Mr Turnbull suggested Mr Joyce had “appalled all of us”, the Prime Minister appeared to suggest there was no need for an investigation.

Asked if he would get Dr Parkinson to examine Mr Joyce’s conduct, he said: “Again, those who believe he has breached ministerial standards or want to believe that, should actually make the case for where the breach has occurred,” he said.

“That, bluntly, is the point.”

Asked during Question Time what had prompted him to order the probe, Mr Turnbull did not answer directly.

“The matter of compliance with ministerial standards is one I take very, very seriously,” he said.

“There were constant claims that the member for New England had been in breach of the statement of ministerial standards but no particulars were being given.

“It was appropriate and I discussed it with the member for New England, then deputy prime minister at the time, that this work would be undertaken and it was undertaken by the Secretary.”

In his initial letter to Dr Parkinson, Mr Turnbull also said he had discussed the decision with Mr Joyce.

“As I reiterated to you, the Deputy PM continues to give me an unequivocal assurance that he has not breached any rules or standards relating to his position as minister,” Mr Turnbull wrote.

“However, to ensure complete transparency, the Deputy Prime Minister and I have agreed that you will examine these matters.

“The Deputy Prime Minister has assured me that he will cooperate with you and provide all information and assistance.”

Mr Joyce, who has continually denied breaching ministerial standards or misusing his travel entitlements, resigned on Friday amid mounting pressure for him to fall on his sword.

Since his affair with Vikki Campion was revealed by The Daily Telegraph, Mr Joyce has come under fire over his decision to approve two new jobs within the Nationals for Ms Campion, and for his use of travel entitlements.

Fairfax Media reported that Mr Joyce charged taxpayers to stay in Canberra while Parliament was not sitting on 50 occasions, far more than any other government minister.

The New Daily revealed last week that he arranged a $6000 RAAF charter flight to get home to Tamworth on Mother’s Day last year, after charging taxpayers to stay in Melbourne for an AFL game the night before.