Foreign Ministry spokeswoman Marzieh Afkham said the publication of the cartoon "provokes the sentiments of Muslims the world over".
"We condemn the blasphemous measure of the French weekly because it will provoke and hurt the feelings of Muslims and could fan the flame of the vicious circle of extremism in the world,” she said.
She underlined the need for respecting the sanctities of all divine religions, criticizing the West-style freedom of expression.
Iran has strongly condemned last week's deadly assault on the magazine's Paris office by extremists who killed 12 people, including much of the weekly's editorial staff and two police officers. Afkham said the attack was against Islam's teachings.
 Al-Qaeda's Yemeni affiliate claimed last week's attack, casting it as revenge for the magazine's earlier publication of caricatures of the prophet deemed offensive.
In remarks on the sidelines of nuclear talks in Geneva, Iran's Foreign Minister Muhammad Javad Zarif called for mutual respect among different cultures.
"We believe that sanctities need to be respected and unless we learn to respect one another it will be very difficult in a world of different views and differing cultures and civilizations," he told reporters.
"I think we would have a much safer, much more prudent world if we were to engage in serious dialogue, serious debate about our differences and then what we will find out that what binds us together is far greater than what divides us."
Zarif said serious dialogue with the West would be easier if it respected Muslim sensitivities.
"Unless we learn to respect one another, it will be very difficult in a world of different views and different cultures and civilizations, we won't be able to engage in a serious dialogue if we start disrespecting each other's values," Zarif said. "We believe that sanctities need to be respected.