"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 different cultures and civilizations," Zarif told reporters before meeting in the Swiss city with US top diplomat John Kerry.
It is a taboo for Muslims to show images of the prophet, and the Iranian foreign ministry had already condemned the cover of the French satirical magazine Charlie Hebdo, saying it was "insulting" and "provocative".
The new issue of Charlie Hebdo is the first since an attack by Islamist gunmen last week at the magazine's office in Paris which killed 12 people.
Iran denounced the massacre the day it happened as being in complete "contradiction" with Islamic teachings.
"We won't be able to engage in a serious dialogue if we start disrespecting each other's values and sanctities," Zarif told reporters on Wednesday as he waited to greet Kerry for talks on Iran's nuclear programme.
"And 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," he added.
"Then we will find out that what binds us together is far greater than that what divides us."
The Iranian minister added that the world was "now faced with very serious problems of extremism not only in the Middle East but unfortunately in Europe.
You've seen demonstrations here in Europe which are extremely dangerous and we need to be able to deal with that."