Two of the planes were headed for the capital Tripoli and the other for Sebha, in the southeast of the country, ministry spokesman Grigoris Delavekouras said on Athens radio.
He said the operation was being led by the secretary of state at the ministry, Dimitris Dollis, who was one board one of the planes, and would evacuate the majority of Greeks living in Tripoli and the Sebha area.
According to the ministry, around 300 Greek nationals are currently in Libya.
In addition, two Greek ferries have been chartered by the Chinese authorities to evacuate some 15,000 of the 30,000 or so Chinese nationals in Libya.
The ships, which left the eastern Libyan port of Benghazi, also took on Greek nationals on the spot, Delavekouras said. They are due to arrive in Heraklion, the main town on the southern Greek island of Crete, in the afternoon.
Two other Greek ferries have also been chartered by China and left Greece on Wednesday. They will also eventually head to Crete, where the Chinese evacuees will then be repatriated by plane.
