John Humphrys has accused The Times of a "grotesque piece of mischievous journalism" for saying he had "nothing but contempt" for Labour ministers.
John Humphrys has denied calling politicians liars
The Times claimed the BBC Radio 4 Today host mocked Labour MPs in an after-dinner speech. Humphrys was subsequently censured by the BBC.
On Thursday he called the Times report "misleading" and said it was not true that he had contempt for Labour MPs.
The Times editor Robert Thomson said its story was "fair and accurate".
The Times reported that Humphrys said the BBC "got it right" in Andrew Gilligan's 2003 report that claimed the government "sexed up" intelligence in Iraq's weapons capabilities.
This report sparked the Hutton inquiry, which led to the resignation of BBC director general Greg Dyke and chairman Gavyn Davies. The BBC subsequently apologised to the government for the allegations.
Following Saturday's Times story, Humphrys said it was a "gross misrepresentation" to say he had called politicians liars and added that he had not said anything he had not said before.
On Thursday he told the Institute of Directors in Manchester: "The Times, having devoted two pages to the attack on me on Saturday, had decided by Monday that it was worth no more than a 'chuckle'.
"That's what its editorial said - the BBC chairman, Michael Grade, 'should read it... chuckle and move on'. How extraordinary."
Mr Humphrys added: "If anyone draws from this farcical business of the past few days the conclusion that the independence of people like me has been restricted, they are wrong.
"Independent journalism is too ingrained in the BBC. It is our lifeblood. It is the main reason for the BBC's existence. It is by a mile the most important thing we do."
On Friday The Times editor Robert Thomson said: "Our coverage was fair and accurate and we stand by it."
He added: "Mr Humphrys said himself that some of his remarks were 'injudicious'.
"Now he has, unfortunately, distorted both the original Times report - which made very clear the mocking nature of his paid-for speech - and the following Times leader, which expressed concern at the personal prejudices of BBC news presentation."