The plane with 81 passengers on board was hijacked when a passenger claiming to have an explosive belt took charge of the plane and directed it to land Larnaca airport, on the south coast of Cyprus.
The Larnaca airport has been closed and scheduled flights diverted elsewhere.
The plane was on its way from Alexandria to Cairo took off from Bourg el-Arab airport just outside Alexandria on Tuesday.
EgyptAir confirmed the hijacking on its Twitter account: "Our flight MS181 is officially hijacked. We'll publish an official statement now."
The hijacker has been indetified as Ibrahim Samaha is a dual American-Egyptian national and he carried the hijack over ex-wife.
Apart from the crew and four foreign passengers all people on board have been released.