Headlined "Germany Then and Now" and appearing under the swastika and the imperial eagle, the advertisement has provoked a furious reaction from Holocaust survivors and the US State Department, and an embarrassed silence from German members of the sect.
"You may wonder why German officials discriminate against Scientologists," the advertisement said. "There is no legitimate reason but then there was none that justified the persecution of the Jewish people either."
The Jews, understandably, were underwhelmed by the comparison. Ignatz Bubis, the leader of Germany's Jewish community, accused the Scientologists of falsifying history. The advertisement, he said, was "an insult to German politicians and especially disparages remembrance of the suffering" endured by his people.
Even the United States government, which in the past had expressed criticism of Bonn's heavy handed treatment of the church, rushed to Germany's defence on this occasion.
"This is an outrageous charge against the German government by an American group," Nicholas Burns, the State Department spokesman, said. "It bears no resemblance to the facts of what's going on there. The language used is needlessly provocative and not constructive, given the history of Germany." The German branch of the church would not comment.
Relations between the Church of Scientology and Germany have been deteriorating since earlier this year, when the Bonn government published a pamphlet accusing the sect of totalitarian tendencies. Several ministers have proposed a ban on the organisation, and an expulsion of church members from the civil service.
During the summer, members of the governing Christian Democrats' youth wing called for a boycott of the Hollywood movie Mission Impossible on the grounds that its star, Tom Cruise, was a Scientologist. The American jazz pianist Chick Corea was barred from performing at a state-sponsored concert in Bavaria for the same reason.