Malcolm Turnbull says he doesn’t know if Barnaby Joyce’s position is safe but agrees the Deputy Prime Minister’s affair with his ex-staffer and now pregnant partner has harmed the government.

While Mr Joyce claims to have the majority support of his party to continue as Nationals leader, Mr Turnbull told 3AW on Monday that he didn’t know if that was the case.

The prime minister was forced to admit the scandal had harmed the government after the latest Newspoll showed the coalition lose the small gain it made on Labor earlier in the month.

“It’s distracting and it’s unhelpful,” he said.

Questions are also being asked about whether Mr Turnbull confronted Mr Joyce about the affair when rumours first began circling, and whether Mr Joyce denied his relationship with Vikki Campion.

“I’m not going to go into the private discussions I’ve had with him other than to say that at no stage did he say to me that he was having a sexual relation with this lady,” he said.

“At no point did he say to me that he was having an affair with the woman in question and he took the view that it was entirely a private matter.”

Mr Turnbull says his wife Lucy has been in touch with Mr Joyce’s estranged wife Natalie since the affair, which he last week labelled “a shocking error of judgment”.

Mr Joyce has called those comments “inept”, but insists he and Mr Turnbull continue to have a strong working relationship.

“Like most people in a strong business relationship, there are times you need to discuss your views because that’s how you resolve things,” Mr Joyce told Fairfax Media on Monday.

“I don’t believe either of us are the sort of people who whisper behind closed doors – if you have an issue, you confront it head on and that’s what we did.”

Two in three voters believe Mr Joyce should quit as Nationals leader, A Newspoll conducted over the weekend and published in The Australian on Monday found.

Mr Joyce rejected ongoing questions about his travel expense and other entitlements, remaining confident there had been no misuse of travel or entitlements.

Mr Turnbull said the Nationals leader had also given him an “absolutely unequivocal assurance” to that effect.

Mr Joyce on Monday began five days personal leave after a tumultuous week that culminated in the public falling out with Mr Turnbull and murmurings about his position as Nationals leader.

With Mr Turnbull and deputy Liberal leader Julie Bishop also away, Finance Minister Mathias Cormann will be acting prime minister.

– AAP