Sir Jeremy Heywood, the country's top civil servant, has said he suspected there was a "gigantic conspiracy" behind the row that led to the resignation of Andrew Mitchell, but did not investigate further because it was outside of his remit.
The cabinet secretary told MPs on Thursday that CCTV footage of the incident showed "inaccuracies and inconsistencies" in emails sent by someone who claimed to have seen the September altercation, which meant they should not be relied upon in deciding whether Mitchell should be sacked.
“We accepted that there were unanswered questioned, including the possibility of a gigantic conspiracy or a small conspiracy. There were unanswered questions, but we decided on balance to let matters rest as they were; decided to stick by Andrew Mitchell, keep him in post and move on,” Sir Jeremy said.
Mitchell was forced to quit in October 2012 after he was accused of swearing at police officers at the gates of Downing Street. He was also accused of calling them "plebs", a charge he has repeatedly denied.
The emails that backed up the police account of the disputed incident later turned out to have been sent by a serving police officer rather than an ordinary member of the public.
Asked by incredulous MPs why he did not consult the police log and challenge its version of events before reporting back to David Cameron, Sir Jeremy said: "I can only do what I am asked to do. It's not the role of a civil servant or the cabinet secretary to start investigating the police.
"That's not my job. I don't have the powers, I don't have the expertise, it wouldn't be right for the cabinet secretary to be involved in that sort of thing.
He added: "The investigation into whether these emails were reliable or not was totally within my remit and competence."
Sir Jeremy also revealed he did not investigate whether Mitchell had used the word "pleb", the key toxic phrase Mitchell was accused of hurling at police that led to his resignation.
The cabinet secretary said it was not "appropriate or necessary" for him to look at the police log of the incident, because it was "not material to my conclusion" that the emails were unreliable.
"I did not look into the question of whether the word 'plebs' was used," he said. "There was a genuine difference of opinion on that, and the CCTV footage doesn't bear on that one way or the other."
And he added: "I was very comfortable with the time and resources that I had for my review, and I was very confident with my conclusion."
Cameron insisted that the chief whip should not lose his job over the incident, as he had apologised to police for swearing, Mitchell eventually resigned in October after weeks of controversy.
Sir Jeremy today told the House of Commons Public Administration Committee that the prime minister had only asked him to look into the emails and it was not his role to investigate the police.
He confirmed that he did not meet the sender of the emails, did not ask to see the police log and did not pass on his concerns about the emails to the police. A Metropolitan Police inquiry is currently under way into the emails, following allegations that they were sent by a serving police officer posing as a member of the public.
Sir Jeremy faced challenges from committee members, including chairman Tory MP Bernard Jenkin, over whether someone in his position should even have been asked to carry out an inquiry into the incident.
Jenkin told him: "You are just the wrong figure to conduct such an investigation. Is the cabinet secretary the correct person to conduct such an investigation in the midst of intense media furore, while there are contested accounts on which the career of a senior minister turns? You are not equipped to carry out the right investigation. You didn't get to the truth about that email.
"You lost a minister because of false allegations about him that were not properly investigated."
But Sir Jeremy insisted that Mitchell's departure was not a result of his inquiry, and said it was not for him to suggest to the Prime Minister that his probe should be widened to look into the veracity of the police account.
The cabinet secretary told the committee: "It's a perfectly legitimate part of my role and frankly, I think I did the job competently and came to the right conclusion."
He said that once police investigations are complete, Downing Street would "take stock" of its response to the Mitchell affair.
But he said it was too early to do so now: "Clearly there are a number of very serious unanswered questions here, not least the allegations that there have been about the leaking of Number 10 police logs to the media and continuing allegations that the logs were falsified in some way - absolutely not proven, but allegations.
"These are very serious allegations. It is very, very important that the people guarding 10 Downing Street are people of integrity. If it is proven in a court of law - if it gets to that - that someone has tried to falsify evidence to bring down a Cabinet minister, that is a very fundamental issue, so I think it would be wrong to rush to judgment now."