The German Bishops' Conference said in a press statement that rape victims treated in Catholic hospitals should "of course receive humane, medical, psychological and pastoral care."
"The administration of a 'morning-after pill' can be part of this so long as it has a preventative and not an abortive effect," added the bishops.
They specified: "Medical-pharmaceutical methods, which result in the death of an embryo, should continue not to be used."
German bishops said after a meeting in the western city of Trier that they trusted Catholic institutions to take the correct medical decisions "on the basis of this moral and theological guideline."
"In every case, the decision of the woman concerned must be respected," added the statement.
The bishops were considering the issue after a woman who had been raped was turned away by two Catholic hospitals in the western city of Cologne. The Catholic Church is fundamentally opposed to contraception or abortion.