A lack of trust in both politicians and journalists is the most serious fall-out from the Hutton report, BBC political editor Andrew Marr said.
The next friction could be over the BBC's charter renewal
After the resignations of the chairman of BBC governors and the director general of the corporation, the issue of the battle between the government and the BBC was over, he told BBC News at Ten.
However he added: "It's certainly not the end of the arguments over why we went to war in Iraq, about WMD or about the 'dodgy' dossier.
"In the end, however, this is about trust. That's the big question for politicians and journalists at Westminster, neither of us terribly trusted."
Marr said it was a question of who people looked to trust.
He said the government looked to Lord Hutton, who said politicians were more trustworthy.
But judging from opinion polls, the public tends to trust the BBC - three to one over the government according to one.
"The truth of the matter is too few of us are trusted at all and that is a matter for politicians and journalists to think about," said Marr.
The next arena for a clash between the government and the BBC could be the BBC's Royal Charter, which is due for renewal in 2007.
Marr was asked if that would lead to renewed friction.
"It's difficult to judge when you're in the centre of it, but this does feel like the worst crisis in the BBC's history.
"There's a lot of emotion, suspicion and jubilation in some quarters.
"The question is how much can that be put aside for a really serious look at the big issues: what's the BBC for, who should pay for it, what should its remit be in the political world?
"Both the prime minister and Tessa Jowell have given pledges that they won't be over influenced by the Hutton procedure and the BBC won't be the only organisation hoping that's true."