Senator McKenzie is under pressure for politicising a $100 million grants program to target marginal seats.

Mr Hunt was less than effusive when asked whether she would still be a cabinet minister when parliament resumes next week.

"I presume that's the case," he told ABC radio on Monday.

"I have no change in my position, I have previously expressed my confidence (in Senator McKenzie), and that hasn't changed."

Former Nationals leader Barnaby Joyce is confident his partyroom colleague will keep her job.

"I have been taking bets with people who have all been running out saying she'll lose her job - no she won't. She will keep her job," he told the Seven Network.

"This will be a rough time in her career, but I bet you she'll see it through."

A damning auditor-general's report into the grants scheme found it favoured seats targeted in last year's federal election.

Scott Morrison has referred Senator McKenzie's handling of the program to his department head Philip Gaetjens to see if ministerial rules were broken.

Australian Associated Press