The pair - whom Ankara wants to extradite as "terrorists" - had been told they were allowed to stay by asylum authorities, although the Greek state contested the ruling.
They are part of a group of eight Turkish officers who arrived in neighbouring Greece after the failed coup, and their fate has strained relations between Athens and Ankara.
Greece's country's top administrative court, the Council of State, on Wednesday found in favour of the co-pilot of the helicopter which flew the men over the border, and the decision also applies to another one of the men.
The judicial source said the Greek government has launched an appeal against the second ruling - the result of which will apply to the next six officers.
The Black Hawk helicopter which carried eight Turkish soldiers who fled to Greece in order to request political asylum. Source: Getty Images Europe
According to their lawyers, the eight wish to leave the country, fearing they could be kidnapped by the Turkish services.
Greece's Supreme Court has already ruled that the eight will not be extradited, arguing that they would not have a fair trial at home.
Ankara says the soldiers are part of the movement led by Muslim preacher Fethullah Gulen, whom Turkey blames for masterminding the coup attempt. The men deny involvement in the coup bid.
A further complication arose in March, when Turkish forces arrested two Greek soldiers who crossed the border whilst allegedly lost in the fog.
They have been incarcerated for the past two months. Turkish President Recep Tayyip Erdogan last month floated the idea of an exchange, which was flatly rejected by his Greek counterpart Prokopis Pavlopoulos.
