The senior civil servant at the Home Office said today that he and former home secretary Jacqui Smith were "shocked and disappointed" to see Metropolitan Police Commissioner Sir Ian Blair forced out of his post by London Mayor Boris Johnson.
Sir Ian announced his resignation last October just days after Mr Johnson took control of the Metropolitan Police Authority. The new mayor had made no secret that he did not have confidence in his top officer.
Today's intervention by Home Office permanent secretary Sir David Normington is a highly unusual step for a serving civil service chief and an indication of how unhappy the department was over Sir Ian's removal.
Speaking on a BBC Radio 4 documentary, The Ian Blair Years, broadcast today, Sir David appeared to indicate disapproval of Mr Johnson's destabilisation of the Commissioner, saying he hoped in future there would be "close co-operation" between the Mayor and the Home Office over the position of Britain's senior policeman.
He recalled how he and Ms Smith - who quit her job in last week's reshuffle - met Sir Ian shortly after a crisis meeting between the Commissioner and the Mayor and recognised he was determined to resign.
Sir David said: "We did debate with him why he had got to this point. I think he believed that, since the Mayor had lost confidence in him, he could not continue. He was fairly resolute that he was going to stand down.
"It was a shock and it was a disappointment. We liked Ian Blair and you had to feel for the human being at the heart of this. This was the pinnacle of his career and he was having to step down from it and he was obviously very upset about that."
In lightly veiled criticism of Mr Johnson's handling of the police chief, Sir David said: "The appointment of the Commissioner and the resignation of the Commissioner is ultimately a matter for the Home Secretary in law and therefore she felt that she should have been consulted about it.
"I would hope that we wouldn't get into that position again and I would hope that there can always be close co-operation with the police authority and the Home Office, the Home Secretary and Mayor on the performance of the Commissioner.
"I hope they can work together."