The Vatican accepted the resignation of Bishop Brendan Comiskey under church rules which require the resignation of a bishop who is "less than able to fulfil his office".
It announced the appointment Dr Eamonn Walshe as temporary apostolic administrator for the diocese, in a statement issued on Saturday morning.
The brief statement in Saturday's Vatican Bollettino said that Pope John Paul II had accepted Dr Comiskey's resignation as Bishop of Ferns in accordance with article 401, par. 2 of the Canon Law Code.
The article in question reads: "A diocesan Bishop is earnestly requested to present his resignation when he has become less than able to fulfil his office due to ill-health or another serious reason."
The Vatican offered no comment on the handling of the Father Seán Fortune paedophile scandal that prompted the Bishop of Ferns to resign.
The appointment of an apostolic administrator, however, underlines the extraordinary and emergency nature of the Vatican measure.
In the past, apostolic administrators have been sent into dioceses where a bishop has fallen foul of the Holy See either for doctrinal infringements or for scandalous behaviour such as the mishandling of diocesan funds or involvement, direct or indirect, in sexual abuse scandals.
The apostolic administrator is directly responsible to the Holy See for his running of the diocese.
Bishop Walshe's appointment is short term, with Vatican expectation being that he will serve as acting Bishop of Ferns for anything from nine months to two years.
Vatican sources say the basic concept underlying the appointment is to meet the immediate demands of a difficult situation while at the same time allowing conditions to mature in which a new Bishop of Ferns can be nominated at a future date, in less controversial circumstances.
Speaking on Saturday after his appointment, Dr Walshe promised to co-operate in any way he could to bring about truth, reconciliation and healing for the sex abuse victims of Father Fortune.
He added that he would co-operate with any inquiry into sex abuse in the diocese.
Last Thursday, the Government announced that there would be a formal inquiry into sex abuse charges against members of the priesthood.
Dr Comiskey, who was still in Rome on Saturday morning, was unavailable for comment.
Vatican sources, however, suggest that he is almost certain to take some time off for reflection prior to taking up a new appointment.
He may perhaps be given a position in his order, the Congregation of Sacred Hearts.