The Syrian government said that Egypt's decision to cut ties with Damascus is an "irresponsible" move led by pressure from the US and Israel.
Egyptian President Muhammad Morsi on Saturday announced "definitive" plans to cut diplomatic ties with Syria and close its embassy in Damascus.
Morsi also called for a "no fly" zone over Syria.
A Syrian government official quoted in state media on Sunday said, "the Syrian Arab Republic condemns this irresponsible position."
The official told SANA that Morsi had joined the "conspiracy and incitement led by the United States and Israel against Syria by announcing the cutting of ties yesterday".
"Syria is confident that this decision does not represent the will of the Egyptian people," the official added.
Egypt made the decision to sever ties amid growing pressure from Sunni clerics to launch a "holy war" against Assad's regime.
The BBC reports that Sunni clerics from several Arab countries met in Cairo on Thursday and issued a statement calling for "jihad to help our brothers in Syria by sending them money and arms".
"The flagrant aggression of the Iranian regime, of Hezbollah and of their sectarian allies in Syria amounts to a declaration of war against Islam and Muslims," the statement went on.
Morsi also demanded that the Lebanese Shia movement Hezbollah withdraw from the fighting in Syria, where its members are assisting Assad's army fight the rebels.
In Egypt, CBS News' Alex Ortiz reports that the Syrian flag still flies over the Embassy in Cairo, for now.
Around 50 Syrian citizens were gathered outside the embassy on Sunday morning, Ortiz reported. Embassy staff or security from inside are calling out names of the Syrians who have come to retrieve their passports, according to CBS.