Whitehall’s top civil servant yesterday challenged Scotland Yard’s decision to go ahead with the cash-for-honours inquiry and insisted that Downing Street had co-operated fully during the investigation.

Sir Gus O’Donnell, the Cabinet Secretary, denied that Tony Blair had threatened to resign as Prime Minister during the 19-month inquiry but said that the investigation, which led to no prosecutions, had been highly distracting for both Mr Blair and his officials.

Giving evidence to the Commons Public Administration Committee, Sir Gus disclosed that he had had to help detectives to get access to e-mail archives without being able to inform the former Prime Minister. Mr Blair had authorised any such move by making clear there should be full co-operation with the Metropolitan Police, he said. He admitted that he had privately raised the issue of leaks to newspapers about the inquiry and had been told they did not come from the Met.

It also emerged that John Yates, the assistant commissioner, had retracted earlier remarks made to the committee denying any contact with political journalists during the inquiry.

Asked what could have been learnt from the £1.4 million investigation, Sir Gus asked the MPs to look at the Met’s decision to go ahead in the first place. “I think the best place to think about this is right at the start and say, ‘Actually, is this investigation worth starting?’,” he said. “It’s at that point I think that you really need the judgment.”

“Given the nature of the legislation, given the nature of what would constitute something which the CPS [Crown Prosecution Service] would say was worth taking to trial, then I think you would need to say it’s at that point you need maximum judgment.” Sir Gus said that Mr Yates had had full co-operation from the Cabinet Office and No 10 despite an earlier assertion from Mr Yates that “certain elements around Downing Street” had not been helpful. The Cabinet Secretary said that he had put someone in charge of dealing with the police after Mr Blair had told him to co-operate fully. All e-mails had been made available to detectives, and staff had helped to retrieve them from the No 10 server, often at weekends.

All e-mails not specifically saved were automatically deleted after a period, but even those deleted could be retrieved from the archives, he said.

“Of course, we were not in a position where we could tell the Prime Minister or other key officials that this was going on, so I had to make some decisions about granting access to those systems . . . but, given the blanket command of the Prime Minister to co-operate fully, that’s what I did.”

It had been “incredibly distracting” for so much to be reported in the media, and he had contacted Scotland Yard on the issue of leaks, Sir Gus said. “I certainly asked them what they felt about the situation and they reassured me the leaks had nothing to do with them,” he told the committee.

Tony Wright, the chairman of the committee, said Mr Yates had written to it, asking to correct the record after he had denied briefing Westminster journalists. Last month Mr Yates said: “I can honestly say that I have never met a lobby journalist.”

Sir Gus’s comments follow publication of a police report claiming that the “most significant” evidence had still not become public knowledge. The Operation Ribble team defends the inquiry as “focused and proportionate” and accuses the Electoral Commission of failing to provide “robust oversight” of the laws on loans to political parties. The report, by Detective Inspector David Jones, also suggests that Sir Ian Blair, the Met Police Commissioner, did have a role, despite his claims that he was kept at arm’s length.

It dismisses allegations of leaks to the media from the investigative team, saying: “This view is confirmed by the fact that the most significant evidence obtained by the investigation has never appeared in the public domain.”

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