German police said they detained the 41-year-old man, who pushed away security guards and crossed a rope barrier to rip off the head of the Hitler figure.
A museum spokeswoman said the headless figure was removed from the exhibition, but she did not know yet if it could be repaired.
About 25 workers spent about four months on the waxwork, which cost about 200,000 euros ($313,000), using more than 2,000 pictures and pieces of archive material and also guided by the Hitler statue at the museum's London headquarters.
Police said the detained man, from the nearby leftist neighborhood of Kreuzberg, appeared to have been opposed to the inclusion of the Nazi dictator in the 75-figure show.
The decision by London-based Tussauds to include Hitler in the museum, which is located on Berlin's premier boulevard, Unter den Linden, has roused fierce passions in the German capital.
Responding to warnings that it might become a site of pilgrimage for neo-Nazis, Tussauds depicted Hitler as a broken man in his bunker just before his 1945 defeat and death.
It is illegal in Germany to show Nazi symbols and art glorifying Hitler and the exhibit was cordoned off to stop visitors posing with him.
Signs nearby ask visitors to refrain from taking photos or posing with Hitler "out of respect for the millions of people who died during World War Two." Camera surveillance and museum officials were meant to stop inappropriate behavior.
London's wax museum has had a Hitler figure since 1933, when he became German chancellor. According to news reports, the London figure, which stands in a heroic posture, has also been damaged, spat on and egged several times.
After being kept behind glass to protect it for 60 years, it was placed in the open in 2002 -- the year when Osama bin Laden's effigy replaced Hitler's as the most hated exhibit in the museum, according to visitor polls.
The Saturday opening of the Berlin museum was extensively reported in the German media. While Hitler has been shown in German school textbooks, television history shows and feature films like "Downfall" (2004), critics said the Tussauds show was using him for entertainment.
Kohl angered by display
Mass-circulation tabloid Bild meanwhile reported on Saturday that another subject of a Tussauds effigy, former Chancellor Helmut Kohl, was seeking legal advice about his own inclusion in the show.
Tussaud's had approached him and he had set certain conditions, but they were not met.
"I never gave permission," he was quoted saying.
Museum official Susanne Keller dismissed the complaint.
"The figures are sent from London," she said. "They do a good job. I assume that Mr Kohl gave his agreement -- that's why he's here."