In defiance of the militants who killed 12 people in an attack on its Paris office, the new edition bears a cartoon of a tearful Mohammed bearing the slogan "Je suis Charlie" ("I am Charlie").
He is shown under the ambiguous title "All is forgiven." Cartoonist Renald "Luz" Luzier said he cried after drawing it.
Last week's murderous attack drew global condemnation, including from several Islamic bodies, but the new cover quickly inspired concerns that it would stir hatred between communities.
Al-Azhar in Cairo, Sunni Islam's most prestigious centre of learning, warned that Charlie Hebdo's cartoons "stir up hatred" and "do not serve the peaceful coexistence between peoples."
Some feel any depiction of the prophet is sacrilege, and Egypt's state-backed Islamic authority Dar al-Ifta denounced "an unjustified provocation against the feelings of 1.5 billion Muslims."
And British radical preacher Anjem Choudary, who is under investigation for alleged links to armed militancy, branded the new publication an "act of war" and a "blatant provocation".
The rector of Paris's mosque, Dalil Boubakeur, urged France's Muslims "to remain calm" over the cover "by avoiding emotional reactions... and respecting freedom of opinion".
The head of a big mosque in central eastern Paris, Hammad Hammami, said: "We consider these caricatures to be acceptable. They are not degrading for the Prophet."
Charlie Hebdo is to print up to three million copies of its "survivors' issue", due out January 14, far more than the usual 60,000 before last week's attack and a historic record for a French publication.
Money from sales will go to the victims' families.
French and Italian versions will be printed, while translations in three other languages -- English, Spanish and Arabic -- will be offered in electronic form, editor-in-chief Gerard Biard said.
Even in Muslim-majority Turkey, the secular newspaper Cumhuriyet was in negotiations to reprint some or all of the French edition of Charlie Hebdo for its readers.
"Turkey is in a difficult period and secularism there is under attack," Mr Biard told AFP, explaining why the talks to produce a possible Turkish version were "the most important."
The remaining Charlie Hebdo staff who put the issue together said putting Mohammed on the cover showed they would not "cede" to extremists wanting to silence them.
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