Malcolm Turnbull has delivered an effective vote of no-confidence in Deputy Prime Minister Barnaby Joyce, announcing he will not be acting prime minister next week, but instead will go on a week’s leave.

This follows Turnbull telling parliament twice earlier this week that the Nationals leader would act in his place when he visits the US next week.

The acting prime minister will be Finance Minister Mathias Cormann, who is the government’s Senate leader. Joyce will be on leave for a week from Monday.

The Liberals’ deputy leader, Foreign Minister Julie Bishop, would normally be next in line, but she is scheduled to be overseas. She did offer to cancel those arrangements, but that option was not taken up.

On Wednesday Joyce shored up his support within the Nationals to continue as leader, but on Thursday he was seriously on the back foot.

In parliament, the opposition pursued his relations with businessman Greg Maguire, who provided him with an Armidale apartment free of rent for six months, worth a total of about A$12,000.

Joyce said that when his marriage had broken down and he was standing for the New England byelection, Maguire approached him and in the discussion offered the accommodation. He had said he would pay, but this was refused by Maguire, Joyce told parliament. He said “he didn’t have to worry about it because I was a mate.”

Maguire has previously told two journalists that Joyce had made the initial approach.

The opposition also asked about a $5,000 payment made by an agency under Joyce’s then-agriculture portfolio to a Maguire business for a 2016 Agricultural Industry Advisory Council dinner at an Armidale hotel that the businessman owns.

Joyce said he did not know about the payment. “Obviously decisions in the vicinity of $5,000 don’t generally go across the minister’s table.”

The Senate late Thursday passed by 35-29 a Greens-Labor motion calling “on the deputy prime minister to resign from his position … for clearly breaching the standards required of ministers; and if he does not resign, calls on the National Party to sack him as leader.”

Earlier, the opposition failed in an attempt to have the House of Representatives call on Turnbull “to immediately sack” Joyce for “clearly breaching the prime minister’s statement of ministerial standards”.

Michelle Grattan does not work for, consult, own shares in or receive funding from any company or organisation that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.