The huge vulture, which has a 6ft 5in wing span, flew over the border from an Israeli game reserve and was caught by Lebanese villagers on January 26.
They became suspicious as the griffon vulture had a tracking device attached to its tail.
The bird is part of a conservation project to reintroduce raptors to the Middle East.
Wildlife officials say the vulture was brought from Spain in 2015 and set free about a month ago in the Gamla Nature Reserve in the Israeli-occupied Golan Heights.
Tel Aviv University is involved in tracking the bird, and as well as a GPS transmitter, it had tags on its wings and an engraved metal ring on its leg saying: “Tel Aviv Univ Israel”.
Wildlife officials in Israel were alerted to its capture when photos of the tied-up bird appeared on social media.
“In a discreet operation with the Lebanese and with the great help of UN forces and the UN liaison unit, the Israel Nature and Parks Authority was able to return the vulture that was caught a few days ago by villagers of Bint Jbeil, Lebanon,” an Israeli statement released on January 29 said.
The Lebanese media says the villagers freed the vulture after it became clear it was not on a spying mission.
After its ordeal the vulture was weak and was being treated for minor injuries, officials said.
However, it is not the first time a griffon vulture has been taken to be an agent of the Israeli spy agency Mossad.
Saudi Arabia captured one, also with a Tel Aviv University tracker, in the desert city of Hyaal in 2011, sparking rumors of a “Zionist plot” that were dismissed by Israeli officials.
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