Tessa Jowell, the culture secretary, was warned that MPs would demand changes to the Communications Bill during its passage through Parliament when the measure won its second reading on Tuesday.
Under the Communications Bill, the BBC will have to comply with the programme standards set by Ofcom but the corporation's governors will remain in the driving seat. Advertisers are demanding a "level playing field" with ITV.
Chris Smith, Jowell's predecessor, told MPs that Ofcom should be given a reserve power to intervene over the BBC. He said that the power of ministers to sack the governors was "a nuclear button option that would never be exercised".
John Whittingdale, the Conservative Party's shadow culture secretary, said the omission of the BBC from the full remit of Ofcom meant the Bill was "fatally flawed", and the Conservative MP Michael Fabricant warned Jowell that it would be wrong to allow the BBC to be its "own judge and jury".
But Jowell replied that the Government had struck "the right balance".
She said: "The onus is very much on the BBC governors to show that they are able to discharge that rigorous and independent role that the House clearly wishes to see."
Meanwhile, 22 MPs have signed a Commons motion attacking a provision in the Bill which would allow Rupert Murdoch to buy Channel 5. They raised concerns that this purchase could "destabilise commercial public service broadcasting".
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