Nationals leader and Deputy Prime Minister Michael McCormack has seen off a challenge for his job from his predecessor, Barnaby Joyce.

Key points: Michael McCormack says he looks forward to "continuing to work with Barnaby Joyce" after the leadership spill

Michael McCormack says he looks forward to "continuing to work with Barnaby Joyce" after the leadership spill David Littleproud has defeated Keith Pitt and David Gillespie to become deputy leader

David Littleproud has defeated Keith Pitt and David Gillespie to become deputy leader Joyce backer and Resources Minister Matt Canavan will lose his ministry and seat in Cabinet

Mr Joyce called for a challenge to Mr McCormack's tenure as Nationals leader yesterday.

Jostling for the leadership began when Bridget McKenzie resigned as deputy leader on Sunday, amid the sports grants saga.

The party has also elected Water Minister David Littleproud to serve as the party's new deputy leader.

"I look forward to working and continuing to work with Barnaby Joyce, who put his hand up for the leadership," Mr McCormack said when he emerged from the partyroom meeting.

"I also continue to look forward to working with Keith Pitt and David Gillespie, who put their hands up for the deputy leader's role."

Mr McCormack has led the Nationals since Mr Joyce lost the job surrounded by scandals two years ago.

Mr McCormack has faced internal criticism about his leadership and had to contend with backbench destabilisation since assuming the role.

David Littleproud becomes the deputy leader after less than four years in the Federal Parliament. ( ABC News: Sean Davey )

"I commend David Littleproud as the newly elected deputy leader for the role he played this very worrying and troubling summer in drought, in bushfires and everything else that has beset regional Australia," Mr McCormack said.

"We will continue as a united team, to put the people of regional Australia first and foremost."

Mr Littleproud, who was elected to Parliament in 2016, held the water and agriculture portfolios until last May's election, after which Senator McKenzie became the agriculture minister.

He now holds the water, drought and emergency management portfolios.

Bridget McKenzie arrives for the Nationals party meeting with Sam McMahon, left, and Perrin Davey, right. ( ABC News: Sean Davey )

"This is a proud day for me. I joined this great party 22 years ago, in my electorate, [in] the little town of Stanthorpe," Mr Littleproud said.

"I believe very much in the values of the National Party. This is about hope, this is about vision for our people in regional and rural Australia.

"This is about now back to business. The shenanigans are over, it's time to get back to looking after those people that are facing drought, that have faced up to the fires. It's time for us to focus on them, not us."

Nationals whip Damian Drum speaks with Barnaby Joyce after he failed to win a leadership ballot. ( ABC News: Sean Davey )

Joyce unapologetic for contesting leadership

Nationals whip Damian Drum told reporters "you will never find out" when asked what the result was from the ballot between Mr McCormack and Mr Joyce.

The victor said he shook hands with Mr Joyce after the result was declared, and vowed to work together to better represent regional Australians.

Mr Joyce avoided the media after the meeting ended. He opted for a written statement to publicly congratulate Mr McCormack.

"I support the vote of the room and will strive for the re-election of a Morrison-McCormack Government as this is definitely the better outcome for Australia and especially of regional people," he said.

"Now my first attentions go back to where they were before this week — New England, drought, fires and now the threat of coronavirus."

Queensland junior minister Michelle Landry said she was disappointed the spill eventuated.

She said she wanted the party to unite behind Mr McCormack and Mr Littleproud and instead focus on supporting regions.

"I wonder why [it] happened because nothing changed," she said.

"We've gone through all this stress within our party and the general public and nothing has changed except staff lost jobs."

Minister loses seat on the frontbench

Matt Canavan takes his backbench seat after resigning to support Barnaby Joyce's leadership bid. ( ABC News: Matt Roberts )

The leadership ballot has also cost Resources Minister Matt Canavan his seat on the frontbench.

He yesterday called Mr McCormack to offer his resignation in order to back Mr Joyce's bid to return to the leadership.

Senator Canavan offered a scathing assessment of Mr McCormack's leadership in announcing his decision on Monday night.

"Matt Canavan has resigned as Resources Minister, I wish him the best," Mr McCormack said on Tuesday.

Bridget McKenzie returns to her Senate leader seat despite losing her agriculture portfolio and party deputy leadership. ( ABC News: Matt Roberts )

That departure, along with Senator McKenzie's resignation, means Mr McCormack will have to promote two Nationals to the frontbench, which will earn them seats in the Cabinet.

Senator McKenzie has retained her position as leader in the Senate, with Senator Canavan as her deputy.

Neither are expected to have portfolios despite holding Senate leadership positions.

Prime Minister Scott Morrison is yet to announce how the Nationals' changes will affect his ministry, particularly the agriculture and resources portfolios.