The BBC's director of news, Helen Boaden, and her deputy, Stephen Mitchell, have stepped aside just two days after the resignation of director-general George Entwistle.
The corporation has also overhauled the "chain of command" overseeing the BBC's journalistic output, in response to a botched Newsnight report.
The BBC has been in crisis as a result of a Newsnight programme which mistakenly implicated Lord McAlpine in a sex abuse scandal and the ongoing issues arising from revelations about Jimmy Savile's abuse.
Mr Entwistle quit on Saturday night over his handling of the growing problems, and there have been calls for Lord Patten, the chairman of the BBC Trust, to follow suit.
Acting BBC director-general Tim Davie has pledged to get a grip of the crisis engulfing the corporation, but said it was too early to take disciplinary action. Speaking to BBC News, he said: "There were some journalistic errors... we've apologised unreservedly... This organisation has lost a very good director-general. We've had an honourable man leave the BBC. My job now is to get a grip of the situation and take action."
Prime Minister David Cameron's official spokesman said it was "hard to justify" the £450,000 payoff to Mr Entwistle. But the spokesman said that Mr Cameron still has full confidence in Lord Patten as chairman of the BBC Trust, and believes his priority should be to offer leadership to the BBC in getting out of its difficulties.
Ken MacQuarrie, the director of BBC Scotland, has delivered a report into the failed Newsnight investigation. But the BBC said the temporary departures of Ms Boaden and Mr Mitchell from their roles were not as a result of the bungled Newsnight programme. Instead, they were in response to the "lack of clarity" surrounding who is in charge while the Pollard Review is making its inquiries. This review - led by former Sky news chief Nick Pollard - is looking into an earlier decision to shelve a Newsnight investigation into Savile's sexual abuse.
The BBC said: "The BBC wants to make it absolutely clear that neither Helen Boaden nor Stephen Mitchell had anything at all to do with the failed Newsnight investigation into Lord McAlpine. Whilst recognising this, the BBC also believes there is a lack of clarity in the lines of command and control in BBC News as a result of some of those caught up in the Pollard Review being unable to exercise their normal authority. In the circumstances, Helen and Stephen will be stepping aside from their normal roles until the Pollard Review reports and they expect to then return to their positions."
Meanwhile, Iain Overton has confirmed that he has resigned as editor of the Bureau of Investigative Journalism in the wake of its involvement in the Newsnight programme which broadcast allegations linking a senior Tory to child abuse. Mr Overton had tweeted before the start of the programme that Newsnight would feature an item, which the BIJ worked on, about a "senior political figure" who is a paedophile.