Prime Minister Malcolm Turnbull last week ordered a high-level investigation into Barnaby Joyce's actions but it has been called off because Mr Joyce has now resigned, it has been revealed.

Key points: PM last week ordered an inquiry into whether Barnaby Joyce breached ministerial standards

PM last week ordered an inquiry into whether Barnaby Joyce breached ministerial standards The head of Prime Minister and Cabinet has called off the inquiry because Mr Joyce resigned from the ministry

The head of Prime Minister and Cabinet has called off the inquiry because Mr Joyce resigned from the ministry Another investigation is still happening into Mr Joyce and his former media adviser, now partner's use of travel entitlements

Mr Turnbull asked the head of his department, Martin Parkinson, to investigate whether the former Nationals party leader had breached any ministerial rules or standards.

Mr Joyce stepped down as deputy prime minister following intense scrutiny over his extra-marital affair, related propriety concerns and a separate sexual harassment claim.

He formally resigned to the Nationals party room on Monday and Michael McCormack was sworn in as his replacement as Deputy Prime Minister and Transport Minister.

Finance Minister Mathias Cormann revealed during Senate Estimates that Mr Turnbull wanted Mr Parkinson to check Mr Joyce's statements that he had not breached any rules.

"The Deputy Prime Minister continues to give me an unequivocal assurance that he has not breached any rules or standards relating to his position as Minister however to ensure complete transparency the Deputy Prime Minister and I have agreed that you will examine these matters," Mr Turnbull wrote to Dr Parkinson last week.

Mr Turnbull said Mr Joyce had assured him that he would co-operate and provide all information and assistance and that Dr Parkinson's report would be considered by the governance committee of Cabinet.

Asked about the investigation during Question Time, Mr Turnbull said it was appropriate and had been prompted by constant claims that Mr Joyce had been in breach of the ministerial standards but "no particulars were being given".

Martin Parkinson was asked by the Prime Minister to investigate whether Mr Joyce breached ministerial standards. ( ABC TV News )

Dr Parkinson wrote to Mr Turnbull yesterday telling him that there is "little to gain" by continuing the investigation in light of Mr Joyce's decision to stand down from the ministry.

But another inquiry is continuing.

The Independent Parliamentary Expenses Authority is carrying out an audit into travel and travel-related expenses by Mr Joyce and his former media adviser Vikki Campion, who is now his partner.

The Opposition used Question Time to highlight the rift between Mr Turnbull and Mr Joyce by repeatedly using the word "inept" in its questions to Government MPs.

More than a week ago, Mr Joyce said Mr Turnbull had been "inept" when he angrily reacted to the Prime Minister strongly criticising him at a media conference.