A 41-year-old Berliner had been arrested and faced charges of causing criminal damage and bodily harm after he hit another visitor who tried to stop him, spokesman Uwe Kozelnik said.
"He wanted to protest against Hitler's figure being on show," Kozelnik said, adding that the model had been withdrawn from display for repairs.
The decision to portray the Nazi dictator among the 70 famous figures in German history in the museum has proved controversial in the country.
In order not to give the impression that Hitler was in any way a figure to be revered, he appears as a broken man in a mock-up of his bunker just before final defeat at the end of World War II.
Ironically he is behind a table, with the aim of preventing visitors to the museum in central Berlin from damaging the waxwork, or posing for photographs with it.
"While we were planning the exhibition, we did surveys on the street with Berliners and with tourists, and the result was quite clear that Hitler is one of the figures that they want to see, " spokeswoman Natalie Ruoss said.
"Seeing as we are portraying the history of Germany we could hardly have left him out ... we want to show the reality," she said.
Stephen Kramer, general secretary of the Central Council of Jews in Germany, believes some Holocaust survivors might find the exhibition offensive but said he was not opposed as long as it was done properly.
"Hitler should not become a tourist attraction but if this exhibition helps to some extent normalize the way of dealing with Hitler, as a kind of a demystification, let's try it," Kramer told AFP in late May.
The other 74 waxworks are less controversial, although for foreign visitors many of the figures from German history, culture, sport and entertainment might cause some head-scratching.
Albert Einstein needs no introduction, nor does the current pope, and most people will have heard of Angela Merkel, Otto von Bismarck, Oliver Kahn and Ludwig van Beethoven.
Others that many will have heard of but might not recognize include writer Guenter Grass, playwright Bertolt Brecht, post-war politician Konrad Adenauer, and the anti-Nazi resistance heroine Sophie Scholl.
Non-German waxworks on display include the Dalai Lama, Winston Churchill, US President George W. Bush and former Soviet leader Mikhail Gorbachev.