Godfrey Bloom, who sits in the European Parliament, had "gone too far", UKIP leader Nigel Farage said earlier.
Farage, who had earlier given a speech to UKIP's annual conference, told the BBC before the decision: "My recommendation is that we now today remove the party whip."
He said 63-year-old Bloom's behaviour had been "selfish" and was overshadowing "all the good things" happening at the conference.
Farage added: "The trouble with Godfrey is that he is not a racist, he's not an extremist or any of those things and he's not even anti-women but he has a sort-of rather old fashioned territorial army sense of humour which does not translate very well in modern Britain."
The whip was withdrawn after a formal disciplinary hearing.