"It is neither reasonable, nor logical, nor wise to publish drawings and films offensive or attacking the prophet of Islam," the International Union of Muslim Scholars, based in Qatar and headed by preacher Yusuf al-Qaradawi, said in a lengthy statement.
The new issue of the satirical magazine, published on Wednesday, features a cartoon of the Prophet Mohammed on its cover holding a "Je Suis Charlie" sign under the headline "All is forgiven".
It was the first edition of the magazine to be published since Islamist gunmen killed 12 people in an attack on its Paris offices last week.
According to the International Union of Muslim Scholars, publication of the drawing would give further "credibility" to the idea that "the West is against Islam".
It added that the images would further "stir up hatred, extremism and tension".
The statement, published late on Tuesday, continued: "If we agree that (those who committed the attacks) are a minority that do not represent Islam or Muslims, then how can we respond with actions that are not directed against them, but against the prophet worshipped by a billion-and-a-half Muslims?"
Al-Qaradawi, 88, is an influential Islamic scholar and is seen as a spiritual guide of Egypts banned Muslim Brotherhood, the movement of ousted former president Mohamed Morsi.
Similarly, a prominent Saudi cleric, Sheikh Ahmed al-Ghamedi, told AFP that publication of the latest image was a mistake.
"Its not a good way to make the people understand us. Jesus or Moses, all messengers (of God) we should respect," and should not be made fun of in pictures or words, Ghamedi said. "I believe it will make more problems."
The magazine, which normally has a print run of around 60,000, said on Wednesday that it would print five million copies this week because of unprecedented demand. The magazine sold out across France within minutes of publication on Wednesday.(*)