The singer caused a number of attendees at her New Orleans show to react unhappily after being told to vote for the incumbent president.
"I don't care who you vote for as long as you vote for Obama," she said.
After receiving a mixed response of cheers and boos, the music legend changed her message.
"Are they booing me?" she said.
"Seriously, I don't care who you vote for as long as you take responsibility for the future of your country. Do not take this privilege for granted. Go vote."
Madonna was recently revealed to be the biggest-selling female singles artist in UK chart history, followed by Rihanna and Kylie Minogue.
The singer confused fans last month when she called Obama a "black Muslim" during a concert in Washington DC.