Mr Joyce will now be a backbencher and Mr McCormack will be promoted to Cabinet.
Labor's Andrew Leigh said Mr McCormack's selection represented a return to some of the lower key leaders of the past of a party he pilloried as one of "squatters and show-ponies".
Rodney Croome, the spokesperson for Just.equal said: "Many LGBTI Australians will be justifiably concerned about Michael McCormack being our Deputy Prime Minister given his hateful comments against us in the past".
He has been battling scandals that started earlier this month with his admission of an affair with a former staff member, who is pregnant with his child.
"I expressed my views on the need to change the current political direction the Nationals are moving in, in a Facebook post over the weekend".
His most strident public backer for the leadership, Victorian MP Darren Chester, was also a journalist.
The Nationals deputy leader Bridget McKenzie has rebuffed suggestions the Nationals leaked the identity of a Western Australian woman who lodged a sexual harassment claim against Barnaby Joyce.
After weeks of controversy, Barnaby Joyce is set to formally resign as leader of the Nationals and Deputy Prime Minister today.
"George has been a friend of mine and will continue to be so", the Riverina MP said. "I will honour the faith and trust and responsibility by always doing my best", he told reporters.
This phone's camera pops up to take your selfie -- for reals
All of these three combined mean that the front face of the phone is, essentially, all-screen - no notch, no anything. It's always nice to see a company that's willing to try new things and the APEX certainly looks like a killer device.
When it came time for the Nationals party room to vote, David Gillespie - the main opponent to frontrunner Michael McCormack - withdrew from the race.
Barnaby's resignation comes after it was revealed he is expecting a baby with his former staffer Vikki Campion.
However, a 1993 column has been brought up in his opposition, in which he blames gay people for AIDS and urged for Pride Parades to be stopped.
Federal Member for Capricornia and Chief National Party Whip, Michelle Landry, welcomed the election of Michael McCormack as Leader of the National Party team.
Asked if he would get Dr Parkinson to examine Mr Joyce's conduct, he said: "Again, those who believe he has breached ministerial standards or want to believe that, should actually make the case for where the breach has occurred", he said.
"I wish him well into the future and I look forward to him being part of our strong National Party going forward".
Mr McCormack, 53, was confirmed as Nationals leader at a partyroom meeting on Monday morning in Canberra having been challenged by George Christensen.
"In light of Mr Joyce's decision to step down from the Ministry, I have concluded that there is little to be gained from continuing this investigation", Dr Parkinson's letter to the PM said, according to Senator Cormann.
"I would like to announce that we had a contested leadership ballot".
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