"Our solidarity with the struggle of the Syrian people against an oppressive regime that has lost its legitimacy is an ethical duty as it is a political and strategic necessity," Ahram Online quoted Morsi as saying.
"We all have to announce our full solidarity with the struggle of those seeking freedom and justice in Syria, and translate this sympathy into a clear political vision that supports a peaceful transition to a democratic system of rule that reflects the demands of the Syrian people for freedom."
The Syrian delegation, including Foreign Minister Walid Muallem, stormed out, Israel Radio reported.
Morsi arrived in Tehran early Thursday after visiting China. It is the first time an Egyptian leader has visited Tehran since the Islamic Revolution in 1979. Tehran cut ties with Cairo after the latter signed a peace treaty with Israel.
Prior to leaving Beijing, Morsi outlined his plans for Egypt's future, saying he plans to build nuclear power plants, the Hebrew language daily Yedioth Ahronoth said.