Downing Street refused to field a Cabinet minister on BBC One's Question Time this week because the panel featured former Labour spin doctor Alastair Campbell, the flagship current affairs programme has claimed.
Gavin Allen, the show's executive editor, said Number 10 had offered to put up a senior minister but only if Mr Campbell was replaced by a member of the shadow cabinet.
"It is a fundamental principle of our independence that politicians cannot dictate who sits on the panel," he wrote in a blog post.
"It is for Question Time, not for political parties, to make judgments about impartiality and to determine who is invited to appear in the interests of the audience.
"Parties are free of course to accept or reject those invitations, but they do not have a right of veto over other panellists. Licence fee payers rightly insist that the BBC must be free from political interference."
The Tories were represented on the panel for the programme by John Redwood, a backbench MP who only this week demonstrated his independence from the Government by voicing his opposition to its plans to increase capital gains tax.
Susan Kramer, a former MP who lost her seat on May 6, appeared for the Liberal Democrats.
Mr Campbell accused the coalition Government of trying to "bully" the BBC and taunted Downing Street's new communications director Andy Coulson for being "totally incompetent". Mr Campbell was himself communications director under Tony Blair.
"I was genuinely surprised - and so was the audience - when David Dimbleby announced that the Government refused to field a minister unless I was not on the panel. I thought I was supposed to be the control freak," Mr Campbell said.
"This pathetic ploy to bully the BBC suggests that the ministers are a bunch of wimps and the Downing Street communications director is totally incompetent. I often found Question Time uncomfortable viewing when doing that job but the idea of not having a senior minister in the week of the Queen's Speech makes a mockery of the Cameron-Clegg claims to be promoting a new politics of engagement."