The Top Gear presenter Jeremy Clarkson is at the centre of a new controversy after again making offensive comments about the prime minister in front of the BBC2 show’s studio audience.

Clarkson, who previously had to apologise to Gordon Brown in February after calling him “a one-eyed Scottish idiot”, described him as a “cunt” in not-for-broadcast comments during the recording of this week’s Top Gear programme on Wednesday night.

The BBC2 controller, Janice Hadlow, was present at the recording and is said to have confronted Clarkson about the remark. A BBC spokeswoman confirmed the pair had a “conversation”, but said the issue was now over.

“There was a discussion about the programme,” she said. “It is certainly not an ongoing issue.”

It is understood that Hadlow did not ask Clarkson to apologise for the incident.

In a further statement, the BBC said: “Janice went to watch a recording of Top Gear as it is BBC2′s top-rated programme, and as controller of BBC2, she holds both the programme and Jeremy in high regard. After the recording, she and Jeremy had a discussion about the programme as controllers and presenters often do.”

At the filming of the previous week’s programme, on 15 July, Clarkson also used the same word to describe Brown as part of a joke, one person present told the Guardian. This remark was not included in the transmitted version of the show on Sunday 19 July.

“Clarkson was talking about a government policy and said as his payoff line: ‘The reason you can’t do that is because Gordon Brown is a cunt,’ ” the eyewitness said. “Everyone found it very funny.”

Downing Street declined to comment, although the Conservative MP John Whittingdale, the chairman of the House of Commons culture, media and sport select committee, criticised the presenter.

“Many people will find that offensive, many people will find that word in particular very offensive,” he said. “I am surprised he felt it appropriate to use it.”

Clarkson, who is currently in Belfast filming for Top Gear in the city’s new sewer system, could not be contacted for comment.

During a press conference in February in Australia, Clarkson courted controversy by using personal remarks to criticise Brown’s handling of the global financial crisis.

“We have this one-eyed Scottish idiot who keeps telling us everything’s fine and he’s saved the world, and we know he’s lying but he’s smooth at telling us,” he said.

Brown lost his sight in one eye in an accident playing rugby as a teenager. Clarkson was forced to apologise after a barrage of criticism from politicians and disability groups. “In the heat of the moment I made a remark about the prime minister’s personal appearance for which, upon reflection, I apologise,” he said in a statement at the time.

The controversy was just the latest to hit the 49-year-old presenter, who is one of the star attractions of Top Gear, which regularly pulls in more than 6 million viewers.

In November last year, he suggested that truck drivers only cared about fuel prices and murdering prostitutes, drawing hundreds of complaints.

The presenter and his Top Gear co-hosts were also condemned by the BBC Trust in July last year for “glamorising the misuse of alcohol” by drinking at the wheel during a polar special.

The trust’s editorial complaints unit said the edition broke its guidelines after Clarkson and James May were shown drinking gin and tonics as they attempted to drive a pickup truck to the magnetic north pole.