The singer was supposedly jeered after playing a set lasting only 45 minutes. Audience members are said to have thrown bottles at the stage and shouted: "We want our money back!"
In a statement on her official website, the star has since blamed the incident on "a few thugs" who were pretending to be fans.
"Playing the Olympia was a magical moment for me and it was real treat to do this special show for my fans and be so close to them," she said.
"Unfortunately at the end of the show - after I left the stage - a few thugs who were not my fans rushed the stage and started throwing plastic bottles pretending to be angry fans. The press reports have focused on this and not the joyous aspect of the evening.
"But nothing can take away or ruin this very special evening for me and my fans. When I looked out in the audience, everyone I saw had a smile on their face. I look forward to having this wonderful experience again."
A rep for Madonna has also defended the show, describing it as a "heartfelt thank you to France".
The incident is the latest in a series of controversies during the 'MDNA' tour. Madonna has previously compared right-wing French politician Marine Le Pen to the Nazis, made a dig at Lady GaGa by performing a mash-up of 'Born This Way' and 'Express Yourself', and flashed various body parts.
Photo gallery - Madonna's most controversial moments:
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