The exhibition was originally co-sponsored by the Israeli Embassy in Warsaw, but it withdrew funding.
Anna Chipczynska, president of Warsaw's Jewish community, visited the museum last week.
She said: "It is disturbing for a viewer once they realise that the tag is played in such a horrific place. The sensitivity of the place, the respect for the people murdered there and for those who survived the Shoah should be enough to understand that this type of work is very inappropriate."
Efraim Zuroff of the Simon Wiesenthal Centre said the video was "the most disgusting thing I've seen in a long time.
"They lied about it. It is just revolting and a total insult to the victims and anyone with any sense of morality or integrity."
A museum spokeswoman claimed the piece carried a warning that it was "controversial" and should only be seen by adults.
A museum director wrote to the Yad Vashem Holocaust memorial in Jerusalem to claim the work had been "misinterpreted".
