The resignation was jointly agreed to after Joyce told the north Queensland MP he had to make a choice between saying things independently of the party or keeping the whip’s job, AAP understands.
It will take effect from Thursday when Nationals MPs and senators will meet to elect a replacement.
Christensen said his position had become untenable after speaking out on several issues in recent months.
But he insisted it was his decision to step down.
“I fell on my own sword, there was no one pushing me to quit. I had to go,” the MP told the ABC.
“I just believe that the situation has probably become untenable – as the person that’s supposed to be standard bearer of discipline with the party to be out there talking against some of the government policies as strenuously as I have been.”
Christensen famously posed for a photograph wearing a shearer’s singlet and holding a stockwhip given to every Nationals whip since 1917.
In the November Fairfax media profile, Joyce said Christensen had great potential and there was no reason he couldn’t be a cabinet minister in the future.
Since then, there has been speculation he may follow renegade Liberal senator Cory Bernardi in quitting the Coalition.
Christensen hosed down those rumours as recently as Monday, saying he would stick with the Nationals.
Nevertheless, he has been outspoken on issues such as the treatment of cane growers in his electorate of Dawson, immigration, and the need for a serious inquiry into banks.
On Tuesday morning he indicated he was willing to cross the floor and vote for a Greens move for a parliamentary commission of inquiry into the banking sector.
“I just think we need to go forward, and to vote for a bill that the government might not support doesn’t mean that I’m against the government,” he told ABC radio.