"This insult has hurt the feelings of nearly two billion Muslims all over the world. The cartoons and other slander damage relations between the followers of the (Abrahamic) faiths," he said in a statement.
The mufti, who oversees Jerusalem's Muslim sites including Islam's third holiest, the Al-Aqsa mosque compound, slammed the "publishing of cartoons ridiculing the Prophet Mohammed, peace be upon him, and the disregard for the feelings of Muslims."
The first issue of Charlie Hebdo after jihadists killed most of its journalists in Paris on January 7 was sold out within hours across France on Wednesday.
The magazine, which has published controversial cartoons of Mohammed in the past, once again featured him on its cover -- but with a tear in his eye, holding a "Je suis Charlie" sign in solidarity with the publication under the headline "All is forgiven".
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Distributors quickly announced the print run would be increased from an initial three million -- dwarfing Charlie Hebdo's normal run of around 60,000 copies. It will also be available in English, Spanish, Italian, Arabic and Turkish.
Al-Qaeda's Yemen branch (AQAP) claimed responsibility for the attack by Islamist gunmen on the magazine's offices in the French capital that left 12 people dead including the country's best-loved cartoonists.
Some other global Muslim leaders have criticised the new cartoon, with the Qatar-based International Union of Muslim Scholars saying "it is neither reasonable, nor logical, nor wise to publish drawings and films... attacking the prophet of Islam."
But many have taken a nuanced stance and tried to calm tensions.
Mufti Hussein also condemned "attacks against innocent people, and terrorism in all its forms.
"Islam renounces the practice of violence against innocents, whether they are Muslim or anything else," he said.