As Muslim demonstrators attacked western institutions across the world, Jacques Chirac, the French president, condemned the "overt provocations" by the magazine.
French Muslim groups tried to prevent Charlie Hebdo from reprinting 12 cartoons first run by Denmark's Jyllands-Posten, images they consider blasphemous, but a court rejected their case on Tuesday on a technicality.
France has a Muslim community of five million, the largest in Europe.
"I condemn all obvious provocations which could dangerously fuel passions," a spokesman quoted Mr Chirac as telling a government meeting yesterday.
"Anything that can hurt the convictions of someone else, in particular religious convictions, should be avoided. Freedom of expression should be exercised in a spirit of responsibility," he said.
Charlie Hebdo carried the new cartoon on its front page, depicting Muhammad burying his face in his hands and saying: "It's hard to be loved by fools."
Sales of the weekly were brisk in Paris. Inside pages showed the 12 cartoons and included an editorial explaining the decision to reprint them.
Philippe Val, the editor, said: "It is unacceptable that religious groups are setting down the rules for the rights of the press and freedom of expression.
"It is not up to religious groups to decide what to publish or not."
In addition to the Danish cartoons, Charlie Hebdo printed drawings on its back page which caricatured other religions, including Christianity and Judaism.
Asked whether he was afraid, Mr Val said: "I think individuals are allowed to have fears. That's legitimate. On the other hand, institutions have no right to express fear."
Charlie Hebdo, which normally prints around 100,000 copies, had printed 320,000 copies of this edition and might now produce up to a total of 500,000 copies, journalists at the magazine said.
Meanwhile, Condoleezza Rice, the US Secretary of State, accused Iran and Syria of deliberately stoking Muslim anger in the dispute.
"Iran and Syria have gone out of their way to inflame sentiments and to use this to their own purposes and the world ought to call them on it," Ms Rice said at a joint news conference with Israel's foreign minister.
Earlier, George Bush, the US president, said governments should stop the violence that has erupted over the cartoons, including attacks on western diplomatic missions in parts of the Muslim world.
Such violence was evident again yesterday, though not as fierce as in previous days. Dozens of international observers abandoned the West Bank city of Hebron after irate demonstrators smashed windows and threw stones at their headquarters.
Afghan police fired at protesters trying to storm a US military base, killing three and wounding 20.
Those deaths, in the town of Qalat, brought the number of Afghans killed in similar protests this week to ten.
Crowds pelted the British embassy in Tehran with stones, smashing several windows and chanting "Death to Britain" and saying they would die for the Prophet.
More peaceful protests were staged in Bosnia and Indonesia.
Din Syamsuddin, a conservative cleric who leads the 30-million strong Muhammadiyah, Indonesia's second largest Muslim group, said: "I urge Muslims not to overreact and act in a violent and anarchist way, because those things are completely against Islamic teachings."
Kuwait's parliament urged fellow Muslims across the world to protest in a calm way, saying that "irresponsible" acts damage Islam. In Iraq, Abdul Aziz al-Hakim, the country's top Shiite political leader, made a similar call for calm in a nationally televised speech.