The woman sprang from the first row, throwing off her leather jacket, during the Christmas service by Cardinal Joachim Meisner and climbed onto the altar.
With the cardinal and worshippers looking on, she was led away by security guards. The woman, named as Josephine Witt, was then held until the end of the service and reported to police for trespassing and disturbing worship.
She had previously been involved in a topless protest against Russian president Vladimir Putin in Hannover and said she wanted to demonstrate against the Catholic church and its power structures. Witt claimed she was hit by the security guards and a member of the congregation.
She said: “Cologne is a stronghold for Catholics in Germany and Meisner represents a very conservative strand.”
The diocese said it did not want to make “a big fuss” about the protest, but the president of the Central Committee of German Catholics, Alois Glück, said: “No argument can justify such actions.”
“These are provocations that ultimately only aim to harm other people," he told the Kölner Stadt-Anzeiger.
The Green Party also criticized Witt's protest. Volker Beck, the party’s spokesman for religious affairs, said: “The action by Femen in Cologne cathedral was disrespectful and an unnecessary disturbance of worshippers during a service.”