The bishops, meeting in the German city of Trier, agreed that Catholic hospitals in Germany should be allowed to prescribe the morning-after pill for women who had been the victims of rape.
However, Germany’s Catholic clergy stipulated that medicines may only be used that prevent conception and not as a means to induce abortion. The use of drugs that cause the death of an embryo or fetus would continue to be banned, even for rape victims, they said.
In a statement issued after the meeting, the bishops said they wished church hospitals 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," the statement added.
While emergency pills can be used to prevent conception altogether, they can also be used to stop a fetus becoming established in the womb.
The church was forced to clarify its stance after the decision of German cardinal Joachim Meisner to allow the use of some morning after pills at church hospital in his Cologne archdiocese. He changed the policy after two church hospitals refused to treat a rape victim by prescribing the pill - a move that attracted national attention.
Meisner said last month that the church was "deeply ashamed by this incident because it goes against our Christian mission."
At the opening of the four-day conference, chairman Robert Zollitsch had appealed for bishops to adopt a joint line to allow some use of the method in light of public outrage about the way the women had been treated.
rc/msh (AFP, AP, epd, dpa)