The De Mata Trick Eye Museum's marketing officer said the statue was removed Friday night following an Associated Press story highlighting outrage from Jewish and rights groups.
Human Rights Watch had denounced the exhibit as "sickening" and the Los Angeles-based Simon Wiesenthal Center, which campaigns against Holocaust denial and anti-Semitism, had demanded its immediate removal.
The museum, which has waxworks of about 80 famous people, had the Hitler figure on display since 2014.
On Sunday, the space at the museum occupied by Hitler was empty and the image of Auschwitz, where more than 1 million people were exterminated by the Nazi regime, was gone.
More From This Section
It was not the first time Nazism and its symbols have been normalised or even idealized in Indonesia, the world's most populous Muslim nation and home to a tiny Jewish community.
A Nazi-themed cafe in the city of Bandung where waiters wore SS uniforms caused anger abroad for several years until reportedly closing its doors at the beginning of this year.