The backbencher confirmed his decision in a statement on Tuesday which said: "It was my decision to resign; and my decision alone. I was not pushed by anyone.”
His decision to relinquish the position will see his annual salary drop by close to $26,000 a year, leaving him with just the base parliamentary remuneration of $199,040.
“I did feel some of my colleagues may have been aggrieved that the enforcer of discipline was being somewhat ill-disciplined himself,” Mr Christensen said.
The maverick MP said Nationals leader Barnaby Joyce had been incredibly supportive and would have supported whatever decision he made.
“I thank him and the rest of the Nationals team for the great honour of serving as their Chief Whip over the last six months,” Christensen said.
His decision comes just a day after an opinion poll revealed he is staring down a challenge from Pauline Hanson's party in his seat of Dawson ahead of the 2019 election.
Just last week the outspoken backbencher pledged his support to the National Party after urgent peace talks with leader Barnaby Joyce.
"I'm loyal to Barnaby Joyce, I'm loyal to the National Party, loyal to the LNP," Mr Christensen said at the time.
Mr Joyce travelled north to persuade Mr Christensen not to leave the party and to ease tensions over a dispute which could see jobs lost in the sugar cane industry.
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It will take effect from Thursday when Nationals MPs and senators will meet to elect a replacement.
Mr Christensen said his position had become untenable after speaking out on several issues in recent months.
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Mr 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, Mr Joyce said Mr 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.
The Nationals will elect a replacement Chief Whip during Thursday's party-room meeting, with nominations closing at 12pm on Wednesday.
Mr 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.
-With AAP
