Helen Boaden, the head of BBC News, and Stephen Mitchell, her deputy, are to step aside in the wake of the Newsnight report which falsely identified a senior Tory as a child abuser.
Their apparent departures from their posts come ahead of a report into the Newsnight programme which mistakenly implicated Lord McAlpine in a sex abuse scandal which is due to be published on Monday.
It follows the resignation of the BBC director general George Entwistle on Saturday which has left the embattled corporation in crisis, amid calls for BBC Trust chairman Lord Patten to follow suit.
The corporations's Business Editor Robert Peston told the BBC in a news report on the departures that neither felt the decision to step aside was the right course.
He said: "I believe Helen Boaden and Steve Mitchell do not agree with the decision to step aside.
"There is a view that in an attempt to look decisive and taking action to stabilise BBC News, Lord Patten and [Acting Director- General] Tim Davie are punishing individuals who may well turn out to be clear of any responsibility for what has happened."
Boaden's position had been in question for several weeks, since the Jimmy Savile scandal erupted early last month when it emerged she had a brief discussion with Entwistle - then BBC director of vision - about a proposed Newsnight investigation into the late DJ's alleged abuse.
There have been repeated suggestions the report was shelved because the BBC had planned tribute programmes to Savile, although the BBC has denied this.
The BBC is reporting that Fran Unsworth, the BBC's head of newsgathering, and Ceri Thomas, the editor of BBC's Radio 4 Today programme, have been asked to fill in for Boaden and Mitchell.
Davie has received a report which Entwistle had commissioned from BBC Scotland director Ken MacQuarrie into how Newsnight came to wrongly implicate former Tory Party treasurer Lord McAlpine in the north Wales children's home scandal of the 1970s and 1980s.
Before he quit, Entwistle warned that it could result in disciplinary action against staff and over the weekend MPs demanded that those directly involved in the broadcast were held to account.
The future of Newsnight also appeared to be in the balance, with the chairman of the BBC Trust Lord Patten warning that there would have to be some "tough managerial decisions".