Nationals MP Darren Chester has blamed Barnaby Joyce's failure to pull two hard-right Queenslanders into line for his decision to take a break from the party.
George Christensen and Matt Canavan have sparked condemnation from Mr Chester, a Victorian MP and leading moderate voice within the junior coalition partner.
Mr Joyce insists he is powerless to stop the outspoken backbenchers from pushing controversial positions on lockdowns and climate change.
Mr Chester said he had become uncomfortable with the party's direction since Mr Joyce returned to the Nationals leadership.
"The party room and the way it's working at the moment is quite dysfunctional," he told ABC radio on Monday.
Dawson MP George Christensen called for two Victorian police officers to be arrested after using capsicum spray on anti-lockdown rioters in Melbourne.
Senator Canavan - a former cabinet minister - provocatively questioned whether the Taliban would sign up to a net zero emissions target as the regime seized control in Kabul.
Mr Chester said Mr Joyce had offered no support in moderating their views despite him raising it publicly and privately.
The former veterans' affairs minister - who Mr Joyce dumped from cabinet for a second time earlier in the year - will not participate in partyroom meetings or group chats.
"It's out of sadness rather than anger. It's a degree of frustration," he told Sky News.
Mr Chester described Mr Christensen's views on COVID, which have included misinformation on face masks and unproven treatments, as off the scale.
He said Senator Canavan's Taliban tweet was disrespectful and offensive.
"The Nationals have a great future for regional values and not extreme right-wing values."
Mr Chester, who has been pre-selected as the Nationals candidate for his seat of Gippsland, intends to contest the next election but will reassess his position with the party next month.
Resources Minister Keith Pitt said he was certain his colleague would return before standing at the next election.
But he said there were a range of views within the Nationals from people representing different parts of Australia.
"How do you stop people from walking up to a microphone and making a statement?" he told ABC radio.
Mr Joyce told the ABC after a partyroom meeting on Monday he would not instruct colleagues what to say, adding Mr Christensen and Senator Canavan had been taken out of context.
He said the party did not have a "hard right-wing agenda", but was a broad church.
"I'd hate to see cookie-cutter politicians," he said.
"The National party is the freest party in politics without a shadow of a doubt."
Nationals MPs Kevin Hogan and Llew O'Brien have previously taken breaks from the party out of frustration before returning.
Labor leader Anthony Albanese said Mr Chester had no faith in the government on climate change.
"If Darren Chester doesn't have confidence in the coalition, in which he was a cabinet minister just a few short months ago, the Australian people shouldn't have either," he told reporters.
Australian Associated Press