Cardinal Cormac Murphy-O'Connor expressed sadness at the claims – which are denied – made against Cardinal Keith O'Brien, leader of the church in Scotland.
Three priests and a former priest have complained to the Vatican about behaviour towards them going back 30 years, according to newspaper reports. They are said to be demanding Cardinal O'Brien's resignation.
Speaking on the BBC's Andrew Marr Show, Cardinal Murphy-O'Connor said: "I was obviously very sad to hear that. The cardinal has denied the allegations, so I think we will just have to see how that pans out.
"There have been other cases which have been a great scandal to the church. I think the church has to face up – has faced up – to some of them very well indeed."
Cardinal Murphy-O'Connor said it was up to Cardinal O'Brien – who is reported to have sought legal advice – "how he faces the allegations".
He pointed out that Cardinal O'Brien was due to retire when he turns 75 next month.
Asked whether the cardinal should still be able to go to the Vatican to take part in the selection of Pope Benedict's successor, Cardinal Murphy-O'Connor said: "That is up to Cardinal O'Brien to decide... it will be up to him, and I think rightly so. The allegations have not been proved in any way, so he will have to decide whether he wants to go."
Cardinal O'Brien, who was born in Ballycastle, Co Antrim, has been the Archbishop of St Andrews and Edinburgh since 1985.
He has been an outspoken opponent of plans to legalise same-sex marriage. He has said he has not yet decided who should be elected as Pope during the conclave, which is expected to be held next month.
The claims emerged just days after Cardinal O'Brien 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 is the only British Roman Catholic cleric able to vote in the upcoming conclave to elect a successor to Pope Benedict XVI following his decision to resign.
He told the BBC: "I'd be very happy if others had the opportunity of considering whether or not they could or should be married."