New Egyptian regulations require visas and security clearances for Syrian nationals.
Ninety-five passengers on a Syrian Airlines flight from Latakia were turned away, along with 55 other Syrian nationals on a Middle East Airlines flight from Beirut and 39 traveling to Egypt on other airlines.
This does not mean restoring full diplomatic relations between the two countries.
In February 2012, Egypt withdrew its ambassador from Damascus.
In June, former president Mohamed Morsi announced the cutting of all diplomatic ties with Bashar Al-Assad's regime, closing both embassies.
The ministry spokesperson said that the recent agreement was made to address the needs of Egyptian and Syrian citizens in both countries.
The countries have agreed to re-open the Egyptian consulate in Damascus and the Syrian consulate in Cairo.
Until May, the Egyptian embassy in Syria had facilitated the return of over five thousand Egyptians from Syria since the conflict started in 2011.
Meanwhile, Egypt has become home to hundreds of thousands of Syrians fleeing the ongoing conflict in their country.
The Egyptian Armed Forces deposed President Mohamed Morsi on Wednesday following nationwide protests which, numbering in the millions, called for his ouster. Judge Adly Mansour, former head of the High Constitutional Court, was sworn in as the country's interim president on Thursday.
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