Barnaby Joyce will take leave next week to avoid an uncomfortable stint as Acting Prime Minister after enduring an excruciating interrogation from Labor over his relationship with a New England millionaire.

Mr Turnbull revealed in question time on Thursday that the Nationals leader would take a leave of absence from February 19 to 25.

The Deptuty PM came under renewed pressure during question time when Labor frontbencher Mark Dreyfus revealed a business owned by Mr Joyce’s friend Greg Maguire had received $5000 in taxpayer funds to hold a government function in 2016.

The revelation came with Mr Joyce already under pressure to explain his decision to accept free use of an Armidale apartment belonging to Mr Maguire.

When confronted by Labor, Mr Joyce told Parliament he was unaware of the circumstances of the payment and would take the question on notice.

“It would not seem surprising in a multi-billion dollar department that I’m not aware of a $5000 payment,” he said. 

But Mr Dreyfus pointed to Senate Estimates documents showing Mr Joyce, who was Agriculture Minister at the time, had attended the Agriculture Advisory Council event at the Powerhouse Hotel in Armidale, which Mr Maguire owns.

“How can the Deputy Prime Minister say he didn’t know when more than 80 people saw him there?” Mr Dreyfus said. 

Reading from his phone in Parliament, Mr Joyce said he had received advice saying the event had been “for a function in Armidale”.

“Obviously decisions in the vicinity of $5000 don’t generally go across the Minister’s table,” he said.

“I’m unaware of any decision that I would ever have made to be part of that decision, and anything beyond that, I will take it on notice.”

Following question time, the Secretary of the Department of Agriculture, Daryl Quinlivan, confirmed in a letter to Agriculture Minister David Littleproud that the department “selected” the venue “in line with our procurement guidelines”.

As Mr Joyce dug in, Labor ramped up its calls for him to quit.

“When will the Prime Minister do as is required under his own ministerial standards and sack the Deputy Prime Minister?” Opposition Leader Bill Shorten said.

Mr Turnbull said he had been given “unequivocal assurances” from Mr Joyce that he had not breached ministerial standards.

He said Labor had failed to prove Mr Joyce had broken the rules.

Mr Shorten said Mr Joyce’s decision to take leave next week was a “vote of no confidence” in the Deputy Prime Minister’s ability to do his job.

Mr Joyce’s office said he would be taking leave as he “wanted to support his family and partner after such intense public focus on personal matters”.

Mr Turnbull and Foreign Minister Julie Bishop are scheduled to be overseas, meaning Finance Minister Mathias Cormann will serve as Acting PM.

Earlier, Mr Joyce defended living rent-free in the Armidale apartment, and denied misleading Parliament with his explanation about the arrangement on Thursday morning.

He had said his friend had offered him the accommodation, but recent newspaper reports quoted Mr Maguire as saying Mr Joyce had been the one to ask for a place to stay.

Labor claimed Mr Joyce had breached ministerial standards because the rules state ministers cannot “seek or encourage any form of gift in their personal capacity”.

But Mr Joyce stood by his statement.

“I did not ring Mr Maguire and ask him for a place for free. Mr Maguire approached me,” he said.

“He made an offer. I offered to pay for it. He said that he didn’t have to worry about it because I was a mate.

“If you just think about it logically, you would hardly ring someone up, ask for something for free, then offer to pay for it, then get it for free. That’s because it didn’t happen.”

Later on Thursday, the Senate passed a motion calling on Mr Joyce to resign.

The motion has no effect but is likely to cause further embarrassment for the Deputy Prime Minister.

-with AAP