The prime minister has said he has a "great deal of confidence" in House of Commons Speaker Michael Martin.
Mr Martin has been criticised for not stopping the Commons office of Tory MP Damian Green being searched as part of a Home Office leaks inquiry.
Gordon Brown told the BBC the Speaker had a "very difficult job" and was doing it "to the best of his ability".
The Lib Dems say a Parliamentary inquiry into the affair has been "neutered" and they will boycott it.
On Wednesday, House of Commons leader Harriet Harman declined to say that she had confidence in Mr Martin.
Her government colleague, housing minister Margaret Beckett, also refused to endorse him, telling BBC Radio 4's Today programme: "It is not for the government to pronounce on the Speaker; the Speaker is elected by the House."
But Mr Brown was asked on BBC Radio 5 Live whether he had confidence in the Speaker and replied: "Yes. It's a very difficult job for the Speaker of the House of Commons because, when the issue arises, he has got to make a judgement based on his knowledge of what's happening in the House of Commons."
He added: "I've got a great deal of confidence in the Speaker. He's got a very difficult job and he tries to do it, and does it, to the best of his ability."
Questioned about Ms Harman's comments, Mr Brown said she had been trying to point out that the government had no say in whether a Speaker should remain in office or otherwise.
It was not as if the government had "some control over the Speaker", he said, adding: "We don't. He is appointed by the whole House of Commons."
On Wednesday Mr Martin gave a statement to MPs to explain how officers were able to enter and search Mr Green's office.
He said one of his officials, the Serjeant at Arms, had signed a consent form allowing the action, rather than requiring police to produce a warrant.
Mr Martin promised that in future a warrant would be needed for all such searches and announced the inquiry by a committee of seven senior MPs.
But on Thursday both the Lib Dems and the Conservatives complained that the inquiry would be dominated by Labour members and not start work until after the police inquiry, and any criminal proceedings, had concluded.
The Lib Dems will not now nominate any MPs to sit on the inquiry committee, announced by the Speaker on Wednesday.
It is understood that Conservative backbenchers will put forward an amendment calling for a committee with no overall majority which would report back in January, irrespective of the police inquiry.
A Downing Street spokesman said they had sought legal advice on the issue, the result of which was that they should hold off on the Parliamentary inquiry while the police probe continued.
Mr Green was arrested last Thursday and held for nine hours by the Metropolitan Police, while all his homes and offices were searched.
Earlier, Home Secretary Jacqui Smith said that no minister had had prior knowledge that he was under investigation or was going to be arrested.
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