RTÉ News & Current Affairs Managing Director Ed Mulhall is to step aside from his role for the duration of the BAI inquiry into the circumstances that led to false allegations being made against Fr Kevin Reynolds by RTÉ.
Editor of Current Affairs Ken O'Shea will also step aside for the duration of the inquiry.
Prime Time Investigates Executive Producer Brian Páircéir and reporter Aoife Kavanagh will not be involved in any on-air programming for this period.
RTÉ said the decision was taken to remove any possible doubt about its objectivity and impartiality.
The board of RTÉ said that when the broadcaster is wrong it must ensure there is no cover-up and no rush to self protection.
It decribed the situation as the most serious editorial question that has arisen since the late 1960s.
Yesterday, the Cabinet requested an independent inquiry into the incident by the Broadcasting Authority of Ireland.
It will report back in two months' time.
RTÉ said this evening that Mr Mulhall made the decision to step aside by agreement with RTÉ Director General Noel Curran.
It said: "These decisions have been agreed in order to remove any possible doubt about the objectivity and impartiality of RTÉ's News and Current Affairs services at this time and are taken without prejudice to any party."
Last week, Fr Reynolds was awarded undisclosed damages and received an apology after RTÉ wrongly accused him of sexually abusing a girl and fathering a child in Kenya.
The next series of the Prime Time Investigates programme has been deferred until editorial reviews have been completed.
Taoiseach Enda Kenny said he welcomed RTÉ's commitment to co-operate fully with the BAI investigation.
He said he was aware RTÉ had decided that some staff should step aside during the inquiry and that was a decision for RTÉ.
Mr Kenny was speaking on his way in to the launch of historian and broadcaster John Bowman's book on RTÉ, Window and Mirror.
Earlier, Minister for Communications Pat Rabbitte said the defamation of Fr Kevin Reynolds by RTÉ has raised grave issues.
Speaking on Morning Ireland, Mr Rabbitte said he could not remember a lapse of such magnitude. He said public anxieties had to be addressed.