Videos on YouTube showed concert-goers shouting "refund", while the US diva came under fire on Twitter from angry fans, some of whom paid more than 250
euros (300 dollars) and queued through the night for Thursday's event.
In a statement posted on her website Thursday, Madonna insisted that "playing the Olympia was a magical moment for me".
"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," she said.
"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."
Madonna's performance at the Olympia was initially greeted with enthusiastic cheers but the mood turned sour as it became clear that the
53-year-old diva was not coming back for an encore after about 45 minutes.
A spokeswoman for the star said she had made an effort to keep ticket prices affordable for the Olympia show, which cost close to a million dollars
The US celebrity website TMZ reported that the Thursday night fracas involved just a few dozen people, including supporters of France's far-right
National Front party.
The National Front has taken legal action against Madonna for screening a video showing its leader Marine Le Pen with a swastika on her forehead during
a concert in Paris earlier this month.