The German doctors' association has sharply criticized the hospitals - St Vinzenz-Krankenhaus and Heilig-Geist-Krankenhaus, while an investigation is being conducted to see if they broke the law.
The 25-year-old woman was seemingly drugged with knock-out drugs in her drink at a party in Cologne in December, and then raped. She woke up on a bank in the Kalk district of the city the morning afterwards, the Frankfurter Rundschau newspaper reported.
An emergency doctor who treated her sent her to a hospital for examination and for the collection of potential evidence. But she was turned away from the one Catholic hospital after another. They had both adopted policies banning doctors from conducing such procedures – because it would entail offering advice about abortion.
Doctors who ignored this rule could expect to be sacked, the Frankfurter Rundschau said.
They even refused to help when the emergency doctor assured them she had already given the woman the necessary advice, and had already prescribed her the morning-after pill to prevent a pregnancy.
A spokesman for the Cologne archbishopric told the paper that Catholic hospitals had a general policy of not offering even emergency contraception. But he said he could not understand why the hospitals concerned had also refused to take the possible evidence from the woman.
On Friday, the Marburger Bund doctors' association (MB) sharply criticized the hospitals, and said they should have at least offered her some counselling. Potential legal steps against the doctors involved were also being checked, the Tagesspiegel newspaper reported.
Rudolf Henke, chairman of the MB, said he had never heard of such a thing, and that he assumed there was at best a serious lack of communication between the hospital managers and the doctors.
"One owed this young woman at least the counselling - and all the counselling," Henke told broadcaster ARD's Morgenmagazin show.
The Catholic foundation which operates the hospitals, the Cellitinnen zur heiligen Maria has apologized to the woman, and said the rules had not been understood by some staff.
The North Rhine-Westphalia state Health Ministry has started an investigation to work out whether the hospitals had broken the law.