The Transportation Ministry began on Thursday night an initiative to retrieve Israelis stranded in Turkey due to airline bans on travel to Ben-Gurion Airport.
Channel 2 reported on Friday morning that around 2,500 Israelis were stuck in Turkey.
Planes from Israeli carriers El Al and Arkia were financed by the state to fly to Athens while a Turkish carrier was transporting Israelis from Turkey to the Greek capital where they would transfer to the Israeli aircraft and from there return to the airport in Tel Aviv.
The measure were devised as Ankara will not permit Israel's national airline to land at its airports to airlift out its citizens.
Turkish Airlines extended its halt of flights to Israel throughout Thursday, following a previous 24-hour travel ban.
"We had decided to halt flights to Israel yesterday, now we decided to extend the suspension for another 24 hours because the risk continues," Turkish Communications Minister Lutfi Elvan told reporters.
The Turkish suspension persisted despite the decision of the US Federal Aviation Authority on Thursday to lift its ban, setting the stage for US and international carriers to resume flights.
Last Friday, the Foreign Ministry issued a travel warning for Turkey, warning Israeli nationals not to visit the country due to the current political climate regarding Israel's offensive in Gaza.
The ministry's official Facebook page said non-vital visits to the country should be avoided and safety precautions must be taken.
Niv Elis and Reuters contributed to this report.