By Nick Assinder
Political correspondent, BBC News website
The head of the civil service, Sir Gus O'Donnell, has appeared to question the decision to launch the cash-for-honours police inquiry which hung over Tony Blair's final months in power.
The Cabinet Secretary said "maximum judgement" over whether to proceed with the investigation should have been taken at the very start of the affair taking into account the chances of it ever going to trial.
Mr Yates was quizzed by the same MPs last month
His remarks came during a probing session in front of the Commons public administration committee on the day it was revealed that the police who led the probe had said the most significant evidence uncovered in the inquiry has not been made public
It was also revealed that that man who headed the inquiry, Assistant Commissioner John Yates, had written to the committee to correct some of the evidence he had previously given to the MPs concerning his contact with political journalists.
The MPs had challenged Mr Yates over leaks during the inquiry and he had insisted they had not come from the police, adding he had never met a lobby (political) journalist.
Sir Gus also told the committee he was "puzzled" at Mr Yates' claim he had not received full co-operation from No 10 during his investigations.
He confirmed an image of computer hard drives had been sought by police to retrieve e-mails from the Number 10 server, adding: "Of course, we were not in a position where we could tell the prime minister or other key officials that this was going on."
And he said the entire affair which lasted for more than a year had proved a major distraction for the prime minister as he had to deal with a stream of headlines "some accurate, some wildly inaccurate".
Sir Gus's evidence, combined with Mr Yates' comments, means the affair continues to create waves even after the CPS decided not to mount a prosecution.
That is probably irritating for all those involved, who had repeatedly denied any wrong-doing in connection with the probe into whether honours were awarded in return for money, or perverting the course of justice.
Mr Blair's final months in power were overshadowed by probe
It also points to the depth of the divisions between Downing Street and the Cabinet Office, and the police inquiry team.
Only days ago, Mr Yates gave evidence to the same committee, insisting his inquiry had lasted so long because some people had refused to co-operate with him.
He refused to name names but said he had come to learn that "Downing Street" had many meanings. He left the MPs and observers to draw their own conclusions.
'Really need judgement'
Now, however, the head of the civil service has suggested Mr Yates never complained to him about lack of co-operation from Downing Street - indeed, he said he had received full cooperation.
And he added: "I think the best place to think about this is right at the start."
Sir Gus said the question Mr Yates should have asked himself was whether the investigation was worth starting.
"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 the Crown Prosecution Service would constitute was worth taking to trial, then I think you would need to say it's at that point you need maximum judgment," he said.
Sir Gus did not spell out exactly what he meant, but the implication seemed clear, particularly to those who had questioned the likelihood of the inquiry going anywhere from the very start.