Ukip's only MP has "residual loyalties" to the Conservatives, Nigel Farage claimed as the tensions at the top of the party spilled over at its annual conference.
The eurosceptic leader insisted he was not involved in any plots to oust Douglas Carswell but made clear his differences with the former Tory after fractures emerged during the gathering at Doncaster racecourse.
Mr Carswell was embroiled in a furious corridor bust-up with Arron Banks, who he accused of threatening to deselect him as MP for Clacton unless he joined the millionaire donor's campaign to leave the European Union.
Mr Banks called the incident a "hissy fit in a corridor" and was later overheard saying the MP was "borderline autistic".
The confrontation overshadowed Mr Farage's keynote speech at the conference in Doncaster where he told activists that the new Leave EU umbrella campaign, led by Mr Banks, would unite eurosceptics.
Mr Carswell is currently a central part of a separate eurosceptic group, Business For Britain (BfB), which has refused to sign up to the overarching organisation.
The Ukip leader said: "I don't really understand what it's about and I don't think Mr Banks should or could purport to represent Ukip in any way at all, he doesn't."
He added: "Douglas may have a slight problem with him, Douglas may have this residual loyalty to his friends in the Conservative Party but frankly given that they haven't made their minds up that isn't very relevant."
Asked about the altercation, Mr Carswell told the Press Association: "I think it's a little bit unusual to go about that by suggesting that Ukip MPs who don't join it should be deselected and I merely, very politely, asked him why he was briefing journalists that unless I supported his campaign I would be deselected.
"It's not very democratic and it's a slightly unusual tactic to deploy in a run-up to a referendum."
He insisted he had not been contacted by Mr Banks about joining the donor's faction and suggested that BfB had a better chance of winning the campaign to leave the EU.
The former Tory said there was "absolutely no question of me being Ukip's MP in Parliament not being part of that cross-party group (BfB)".
Mr Carswell, who is due to address the conference tomorrow, left the conference venue shortly after the incident.
The war of words exposes the divisions between the MP and Mr Farage over Ukip's direction.
Mr Banks said Mr Carswell's refusal to back the Leave EU group put him at odds with the party.
He told the Press Association: "All I said was that, because he is the only Ukip MP, it doesn't mean he provides cross-party support to Business For Britain and if he was saying that was Ukip's backing that would be against whatever decision the party takes."
Asked if he was trying to deselect Mr Carswell, a chuckling Mr Banks replied: "Not this week, no. I can't deselect anybody."
He added: "He was on transmit. He had a few things to say, which he said.
"So, essentially, he wandered off and I said something like 'Stay classy San Diego' and that was it."