Morsi told his supporters in Cairo on Saturday that he decided to “definitively break off relations with the current regime in Syria,” AFP reported.
He also called for foreign support for insurgents in the country.
He added that his government would also be recalling the Egyptian charge d'affaires from Damascus.
In addition, Morsi called on Western states to enforce a no-fly zone over Syria.
The United States has recently announced that it will impose a no-fly zone over Syria and the Pentagon is drawing up plans for the action.
Elsewhere in his remarks, Morsi urged the Lebanese resistance movement Hezbollah to withdraw from Syria. "Hezbollah must leave Syria -- these are serious words. There is no space or place for Hezbollah in Syria."
In late May, Hezbollah Secretary General Seyyed Hassan Nasrallah said that members of the resistance movement were battling the militants alongside Syrian government forces in the strategic border town of al-Qusayr -- an important center and supply route for the foreign-sponsored militants.
On June 5, the Syrian army recaptured al-Qusayr after three weeks of fighting.
The Syria crisis began in March 2011, and many people, including large numbers of government forces, have been killed.