Victorian Damian Drum described Senator McKenzie as a "fantastic" deputy and scolded his party room peers for speaking against her.
“It's really poor form to leak anything out of the party room,” he told reporters in Canberra on October 22.
“There is no excuse, there is never a good time to leak out of the party room.
“They (colleagues) would be crazy if they were (vying for her deputy position). She is just such a fantastic leader.
"Bridget is fine, she's done a great job.”
Senator McKenzie has been the party's deputy since 2017 and became agriculture minister in May. She took over from Nationals MP David Littleproud, who now handles the drought and water portfolios.
The ABC reported rumblings within the party began last week after Senator McKenzie introduced a dairy industry code of conduct, following pressure from One Nation leader Pauline Hanson.
The code was designed to give farmers more market power in their dealings with milk processors and was one of Mr Littleproud's initiatives.
Queensland MPs, who have been lobbying for the code's introduction, were furious after Senator Hanson's demands were met so quickly.
“This is nothing to do with Bridget McKenzie. This is all about One Nation getting credit for something they haven't done,” Mr Drum said.
“The Nationals have done all the work behind the scenes. The Nationals deserve credit for that.
“That's where the anger lies; somehow or other, deals have been done to secure One Nation's vote in the Senate and all of a sudden Pauline Hanson is taking credit for something she hasn't done.”
The Courier-Mail reported Wide Bay MP Llew O'Brien told the Nationals’ party room on Monday that he intended to call a leadership spill, but that never eventuated.
Senator McKenzie, who did not attend the party meeting, said her colleagues hadn't raised the concerns mentioned with her and that she would deal with any such suggestions internally.
Labor frontbencher Murray Watt tried to quiz Senator McKenzie over how long she expected to remain agriculture minister during an estimates hearing on Tuesday. But he was swiftly shut down by committee chair and Nationals senator Susan McDonald. Senator Watt also asked Senator McKenzie if she told Mr Littleproud to "stick to his knitting" over portfolio responsibilities.
“He doesn't look like much of a knitter,” she shot back.
Nationals junior minister Darren Chester admitted there were disagreements within the party but only because of the complex issues at hand.
“These are difficult issues we're working through and occasionally colleagues might bump into each other and have a disagreement, but generally speaking we get on pretty well,” Mr Chester said.
“This is a place where people come to debate big ideas about the future of our nation, and the agriculture portfolio ... is a pretty complex policy area.
“We're going through one of the worst droughts in probably our nation's history and there are a lot of issues that need to be resolved.”