Director-general Mark Thompson has said reports that the corporation's journalists are being muzzled to win government favour are "utterly false".
Mr Thompson said the BBC stood for "impartial, rigorous journalism"
In an e-mail to BBC staff, Mr Thompson said newspaper reports saying that journalists were instructed to keep ministers happy were "preposterous".
It follows a report that BBC chairman Michael Grade wanted to sack presenter John Humphrys over a speech he gave.
Mr Thompson said the report was a "straightforward lie".
He said he was "fiercely committed" to the BBC's editorial independence.
"Using the recent row about John Humphrys as its 'evidence', the pieces claim that the BBC is muzzling its journalism in an effort to keep government ministers happy," said Mr Thompson.
"That is completely false and, indeed, utter nonsense."
The newspaper reports came after a New Statesman article by editor John Kampfner, a former BBC journalist, alleged that BBC chairman Michael Grade had wanted to make an example of Humphrys to placate Downing Street.
Kampfner claimed that Mr Grade and Mr Thompson only changed their minds about sacking Humphrys when newspapers supported the BBC Radio 4 Today presenter.
In his e-mail, Mr Thompson said the claim was "a straightforward lie" as he and the chairman had only discussed launching an inquiry into Humphrys' speech.
The Times newspaper reported on 3 September that Humphrys made remarks about Labour politicians in his speech.
It also reported that Humphrys claimed the BBC "got it right" in a controversial news report that claimed the government "sexed up" intelligence in Iraq's weapons capabilities.
At the time, Humphrys said the Times report was a "gross misrepresentation" and said his comments were not anything he had not said before.
A BBC inquiry last month found Humphrys' comments were "inappropriate and misguided".
Mr Thompson said in his e-mail: "I am satisfied that the report Mark (Byford, Head of Journalism) delivered was objective - and fair to John Humphrys."
John Humphrys made the after-dinner speech in June
He added that there was no bias towards the government.
"A few weeks ago... the Prime Minister made it very clear he was unhappy with some of our coverage of Hurricane Katrina and its aftermath," he said.
"I've defended our coverage to the hilt - I thought it was outstanding."
Speaking on BBC Radio 4's World at One show, New Statesman editor Kampfner said he stood by his story.
"I am entirely confident about the quantity and the quality of the sources," he said.