The prime minister's relationship with his deputy looks irreparably split with Barnaby Joyce calling Malcolm Turnbull "inept" for making critical comments about his affair with a staffer.

Late on Thursday Mr Turnbull said his deputy had made a "shocking error of judgment" by having a relationship with former media adviser Vikki Campion, and humiliated his wife and daughters.

Before heading off on a week's personal leave, Mr Joyce called a press conference in Canberra to tell reporters the prime minister's comments had caused "further harm".

"I believe they were in many instances inept, and most definitely in many instances unnecessary," Mr Joyce said on Friday.

"I listened to it and thought that was completely unnecessary, all that is going to do is basically once more pull the scab off for everyone to have a look at."

Mr Turnbull rewrote the ministerial code of conduct to ban ministers from having sex with staff after Mr Joyce's scandal dragged on for more than nine days.

"I've seen Barnaby's press conference and look I understand it's a very stressful time," Mr Turnbull said on Friday afternoon.

"I thank him for his support for the very important change I've made to the ministerial standards."

When asked how he could possibly work with the prime minister again, Mr Joyce said, "I am intending to make sure that, like all relationships, this relationship gets back onto an even keel."

But Mr Turnbull, who cannot sack the deputy prime minister because he is the leader of a coalition partner, denied he was pressuring the Nationals to sack their leader.

"I have not sought in any way to influence the deliberations of the National party. Neither I nor my colleagues have made any criticism of the National party," Mr Turnbull said.

Mr Joyce said the party disliked nothing more than implied interference in internal affairs.

Labor leader Bill Shorten said the prime minister was powerless to sack his deputy, who had "declare war" on Mr Turnbull.

"Australians have every reason to be angry and frustrated when the two most senior Australian leaders are not focused on anything other than their own jobs," Mr Shorten said.

Mr Joyce said he did not believe people should resign in any job because of personal issues.

He again defended his use of a rent-free townhouse for six months, which was provided to him by friend and businessman Greg Maguire.

Mr Joyce has also been criticised for shuffling Ms Campion to other political jobs, and for his department spending $5000 for a function held at a hotel owned by Mr Maguire.

Nationals MP Andrew Broad said he would wait to see any evidence of an abuse of power before considering a leadership change.

"If I see that and it's clear, well then I'll be one of the people talking about what should be the action as a result of that," he told ABC radio.

Treasurer Scott Morrison said he believed Mr Turnbull and Mr Joyce could work together in the future.

"Our leaders will work together, they'll do it because we believe in the future of our country," he told Sky News.

With Foreign Minister and deputy Liberal leader Julie Bishop overseas, Senate leader Matthias Cormann will be acting prime minister when Mr Turnbull travels to Washington next week.