The magazine, Charlie-Hebdo, cited freedom of expression as its reason for publishing the cartoons which came out in its Wednesday edition.
Jacques Chirac, the French president, condemned what he called the "overt provocations" which he said would only only enflame the situation.
"Anything that can hurt the convictions of someone else, in particular religious convictions, should be avoided," a government spokesman quoted Chirac as saying.
French Islamic organisations had applied for an injunction to have the edition banned for inciting racial and religious hatred, but a court rejected the case on a technicality.
Speaking after the ruling, Fouad Alaoui, a member of the Union of Islamic Organisations of France, said that defending the dignity of one's religion did not mean that one was radical.
The front page of the weekly magazine carried a new drawing of Muhammad. He is burying his face in his hands and saying: "It's hard to be loved by fools".
Inside pages carried the Danish cartoons and an editorial explaining the decision to reprint them.
Philippe Val, the magazine's editor, wrote: "When extremists extract concessions from democracies on points of principle, either by blackmail or terror, democracies do not have long left."
Sources at Charlie-Hebdo said its offices and some staff had been placed under police protection.
As well as publishing the Danish cartoons, Charlie-Hebdo published other cartoons on its back page which caricatured other religions including Christianity and Judaism.