Gordon Brown has come to the rescue of the Speaker amid much ministerial annoyance at the failure of Harriet Harman to do the same.

The Prime Minister has said he has a "great deal of confidence" in Michael Martin, something the Commons leader conspicuously failed to do in a BBC interview last night.

Ministers believe that someone as senior as the Commons Leader should have backed the Speaker, regardless of his behaviour, as the functioning of the parliamentary system was paramount.

Mr Martin is going nowhere for now and the Commons does not work if the person sitting in the Chair does not have authority.

Mr Green was arrested last Thursday as part of a police investigation into Home Office leaks accused of conspiring in or encouraging misconduct in a public office. He was held for nine hours, during which time police searched his home, constituency and Commons offices.

It was the decision to let police into the Palace of Westminster which outraged many Opposition MPs. Mr Martin admitted yesterday that the officers had not produced a warrant, but said that he had not personally authorised the search.

Some ministers believe that Ms Harman, with her reputation founded on civil liberties, is grandstanding. She would argue that it is not her job to voice confidence in Mr Martin or his office. He was chosen by MPs, she would say, and his position depends on whether he has their confidence or not. It is not her job to make up their minds for them.

It is not the first time in this affair that Ms Harman has upset some of her colleagues. Some believed she had cut the ground from under Jacqui Smith last Sunday when she first raised concerns about the nature of the police raid on Westminster at a point when the Home Secretary was refusing to direct any criticism at the police.

It is believed that Mr Brown happily acceded to Ms Harman's request to take the lead in reassuring MPs that their privileges were not under threat.

Mr Brown told the BBC the Speaker had a "very difficult job" and was doing it "to the best of his ability".

But the 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."

Mr Brown was asked on BBC Radio 5 Live whether he had confidence in the Speaker, replying: "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."

Meanwhile, the Home Secretary disclosed during a reply to a Conservative MP in the Commons that other investigations were afoot into government leaks

It is assumed one of these is at the Treasury where there was massive concern over the leaking of the pre-Budget report to The Sun and The Times. No-one was ready to confirm that the police had indeed been called in.

The Damian Green affair prompted more angry exchanges in the Commons today as the Home Secretary defended her role in the affair.

In a statement to MPs, Ms Smith again insisted that she had no prior knowledge that the Shadow Immigration Minister was to be arrested last Thursday.

She said that she backed the right of MPs to do their job and hold the Government to account but the “systematic leaking of Government information” raised issues that struck at the heart of Britain’s “system of governance” and "drove a coach and horses" through Civil Service impartiality.

In an angry reply that goaded the Labour benches into cries of "shame", her Tory shadow, Dominic Grieve, accused Ms Smith of "wilful ignorance" and of "washing her hands" of the responsibilities of her office.

He also insisted that the row had nothing to do with national security, saying : "There is not the slightest evidence of this and the Opposition take the integrity of official secrets as seriously as the Government, despite attempts by Government spokesman to smear and spin to the contrary.”

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