On Tuesday, gunmen attacked the US consulate in Libya’s eastern city of Benghazi, killing US Ambassador Chris Stevens and other three US nationals.
Morsi’s remarks come as clashes continue Thursday, between Egyptian police and angry Muslim protesters, outside the US Embassy as the demonstrators chanted in the streets against the sacrilegious movie.
Security forces fired tear gas to disperse the demonstrators.
Outrage is growing across the Muslim world over the $5-million movie that was financed by more than 100 Zionists.
Egyptian President Mohammed Morsi has condemned "attacks" on the Muslim prophet Mohammed (PBUH) in an anti-Islam film produced by an Israeli-American man in the US.
"We Egyptians reject any kind of assault or insult against our prophet. I condemn and oppose all who... insult our prophet," Morsi, on an official visit to Brussels, said in remarks broadcast by Egyptian state television.
Condemning Tuesday attack on the US consulate in the eastern Libyan city of Benghazi, Morsi also slammed violence and said he cannot accept aggression against any embassy in his country.
"We all know that killing innocent people goes against Islam. The freedom to express opinions and demonstrate... are guaranteed but without attacks on private or public property, diplomatic missions or embassies," he continued.
"It is our duty to protect our guests and visitors from abroad... I call on everyone to take that into consideration, not to violate Egyptian law... not to assault embassies," he added.