Barnaby Joyce has been dumped as Acting Prime Minister next week in a dramatic demonstration Malcolm Turnbull has doubts about his role as his deputy.

"The Deputy Prime Minister is on leave next week," Prime Minister Malcolm Turnbull told Parliament.

The overturning of usual practice when the head of government is absent is a clear indication of the prospect of substantial embarrassment were Mr Joyce to take the job.

Mr Joyce was due to take over the position next week when Mr Turnbull meets with US President Donald Trump in Washington.

The appointment to Acting PM was due to go to the Nationals Leader during uproar over his marriage breakup and relationship with a pregnant former staff member, but instead he will now take a break.

The fill-in PM will now be Government Senate leader Mathias Cormann, Mr Turnbull announced.

The usual second candidate, Deputy Liberal Leader and Foreign Minister Julie Bishop, will be on overseas visits.

The move, in effect a demotion of Mr Joyce, was announced as the Labor Opposition made it clear it would pursue him over claims he had breached ministerial standards in accepting accommodation in Armidale from a businessman friend.

Mr Joyce told Parliament he was not aware his administration had made a $5000 payment to Armidale businessman Greg Maguire, who had given the Nationals leader free accommodation when Mr Joyce's marriage collapsed.

Problems have been piling up for Barnaby Joyce since his relationship with former staffer Vikki Campion was exposed.

"I have to admit I was unaware of that $5000 payment," he said.

The issue of Mr Joyce moving from a central role in a controversy to the job of Acting Prime Minister was discussed over a week, with the Deputy Prime Minister refusing to budge.

It is understood he only relented today.

Mr Joyce said he would check details and return with an answer on notice, but Labor's shadow attorney-general Mark Dreyfuss pressed further.

He asked: "How can the Deputy Prime Minister claim he was unaware of the payment of more than $5000 of taxpayers' money to a business owned by Mr Greg Maguire when the payment was made for an event at the Quality Hotel Powerhouse in Armidale, and the Deputy Prime Minister personally attended many in front of more than 80 witnesses?

"How can the Deputy Prime Minister say he didn't know when more than 80 people saw him there?"

And he said: "Would the Deputy Prime Minister advise the House whether he or his office played any role in selecting his close friend's business to receive more than A$5000 in taxpayers' money, or is the House meant to believe that it was just an extraordinary coincidence that an agency under his administration chose a venue owned by his close friend, out of all the venues in daily?"

Mr Turnbull told Parliament Mr Joyce had given him "unequivocal assurances that he has been scrupulous in ensuring the legitimacy and accuracy for any claim for entitlement to ministerial or parliamentary travel allowance.

"If the members opposite wish to assert that he has breached a clause in the ministerial standards, then they should say so and identify the clause," he said.