Disgraced Cardinal Keith O'Brien, who admitted that his sexual conduct had "fallen beneath the standards" expected of him, "will be leaving Scotland for several months for the purpose of spiritual renewal, prayer and penance", the Vatican said.
His future will be decided by senior colleagues at the Vatican, the Catholic Church said in a statement on Wednesday.
Cardinal O'Brien stepped down from his post as Archbishop of St Andrews and Edinburgh after three priests and a former priest complained to the Vatican about inappropriate behaviour towards them going back 30 years.
O'Brien had previously contested the claims.
The allegations against Cardinal O'Brien emerged just days after he called for the Catholic Church to end its celibacy rule for the priesthood.
He said that many priests struggle to cope with celibacy and should be allowed to marry if they wish.
The cardinal, who was born in Ballycastle, Co Antrim, had been the Archbishop of St Andrews and Edinburgh since 1985.
Ordained as a priest in 1965, he was proclaimed a cardinal by Pope John Paul II in October 2003.
His absence from the conclave to elect the next pope meant that the church in Britain had no vote in the process.
One of Scotland's most outspoken opponents of moves to legalise same-sex marriage, he was last year named "Bigot of the Year" by gay rights group Stonewall.