John Longworth, one of three Brexit Party politicians elected to the European Parliament to represent Yorkshire and the Humber this summer, said the decision was "news to him" and that he hadn't been told by party officials.
He has repeatedly clashed with leader Nigel Farage over the party's approach to Brexit and the election. The former director-general of the British Chambers of Commerce called on MPs to vote for Boris Johnson's Brexit deal despite his leader Mr Farage's stark criticism of the PM's proposals.
He has also called on the party to just stand 20 to 30 candidates, contradicting Mr Farage's position of opposing all sitting Labour MPs.
A statement issued by the Brexit Party's chief whip and MEP Brian Monteith said: "We regret having to remove the Whip, but we have been left with no alternative after John Longworth repeatedly undermined the party's Brexit strategy over the last few months.
"The Brexit Party shall not be deflected from, or undermined in, its campaign to win Labour seats. We are receiving a great reception from disenchanted Labour voters and believe we have a good chance of winning in many seats."
Mr Longworth told The Yorkshire Post: “The withdrawal of the whip is news to me as the Brexit Party didn’t have the courtesy to speak to me about it. I do not know what has precipitated this latest decision, I can only speculate that it may have something to do with a confidential vote in the EU Parliament.
"However, as the vote was taken in camera for timing reasons and I respect the rules of the Parliament I cannot comment further as it was a secret ballot. I will continue to fight for Brexit as an independent.”
Earlier today, speaking at a rally in Kirkby-in-Ashfield in Nottinghamshire, Nigel Farage claimed the Brexit Party was "doing very well" in attracting votes from Labour leavers.
Mr Farage ended his address by telling party supporters: "I am more optimistic about Brexit and what it means and leaving this ghastly club based in Brussels run by these bureaucrats ... I am more bullish and optimistic about it than I have ever been at any point in my life.
"I know this is the right thing to do and I ask you to give us your support over the next eight days."