The BBC's director of news, Helen Boaden, and her deputy, Stephen Mitchell, have "stepped aside" as the UK broadcaster seeks to "address the lack of clarity around the editorial chain of command".
The move comes amid the crisis over child abuse allegations against Jimmy Savile and a report wrongly accusing a politician of child abuse.
Acting director general Tim Davie, who took over the top job at the corporation following the dramatic resignation of his predecessor George Entwistle on Saturday night, is expected to set out his plans to manage the crisis later on Monday.
Boaden and Mitchell had already been asked to give up their responsibilities in connection with any stories related to Savile pending an inquiry into why an investigation by the Newsnight programme into claims of abuse by Savile was dropped last year.
There have been suggestions, which the BBC has denied, that the Newsnight report was axed because it would have clashed with a planned tribute programme to Savile, one of the BBC's biggest stars who died in October 2011.
The inquiry is being led by Nick Pollard, the former head of Sky News.
Allegations that Savile may have abused up to 300 children over four decades, including while working at the BBC, have plunged the broadcaster into crisis.
The BBC's problems were compounded when Newsnight, one of its flagship current affairs programmes, was forced to admit on Friday that a report the previous week implicating a senior political figure in child sex abuse was wrong.
In a statement, the BBC said Boaden and her deputy were stepping aside: "To address the lack of clarity around the editorial chain of command, a decision has been taken to re-establish a single management to deal with all output, Savile related or otherwise."
Entwistle resigned on Saturday after just 54 days as director general, saying he took responsibility for the Newsnight report even though he had not seen it.
The state funded broadcaster confirmed on Sunday that Entwistle would get a payoff of $715,000.
It said the settlement took into consideration that Entwistle would continue working on BBC business, including two inquiries in the child abuse scandal.
John Whittingdale, the chairman of the House of Commons committee on culture, media and sport, said he was surprised by the settlement and has sought an explanation.