The magazine's front cover showed an Orthodox Jew pushing a turbaned figure in a wheelchair and several caricatures of the Prophet were included on its inside pages, including some depicting him naked.
The publication comes in the midst of widespread outrage over an anti-Muslim film posted on the internet. French Foreign minister Laurent Fabius criticized Charlie Hebdo's decision as a provocation and said he had ordered security beefed up at French diplomatic offices in the Muslim world.
Charlie Hebdo's Paris offices were fire bombed last November after it published a mocking caricature of Mohammad. In 2005, Danish cartoons of the Prophet sparked a wave of violent protests across the Muslim world that killed at least 50 people.
Prime Minister Jean-Marc Ayrault issued a statement on Tuesday saying: "In the current climate, the prime minister wishes to stress his disapproval of all excess and calls on everyone to behave responsibly."
France is home to Europe's largest Muslim population. Calls are already circulating on social networks and the Internet for protests on Saturday over an anti-Islam film that was made with private funds in the United States and posted on the Internet.
Last Sunday police arrested about 150 people who sought to take part in an unapproved protest near the US Embassy in Paris.
In the torrent of violence blamed on the film, US and other Western embassies have been attacked in cities in Asia, Africa and the Middle East.
The US ambassador to Libya and three other Americans were killed last week in an attack in Benghazi, and Afghan militants killed 12 people in a suicide attack on Tuesday that they said was in retaliation for the film.