Barnaby Joyce will not fill in for Washington-bound Prime Minister Malcolm Turnbull next week, and instead will take leave as pressure mounts for his resignation.

The Greens, Labor, Derryn Hinch, and the Nick Xenophon Team in the Senate voted for a motion asking the Deputy Prime Minister to resign as Nationals leader for "clearly breaching the standards required of ministers" - and if he does not resign, urging The Nationals to sack him.

Joyce faces scrutiny over his affair with a former staffer who is pregnant with his child, and their travel expenses.  Labor also wants more information about a rent-free apartment he accpeted from businessman Greg Maguire.

Mr. Turnbull during question time said that Finance Minister Mathias Cormann would be acting PM while he is out of the country.  That prompted opposition Labor leader Bill Shorten to question whether Mr. Joyce was able to do his job as Deputy Prime Minister.  "Are we simply meant to believe it is all a big coincidence?" Mr. Shorten asked.

Mr. Joyce's office has confirmed that he asked for personal leave because "he wanted to support his family and partner after such intense public focus on personal matters".