Libyan Foreign Minister Najla Mangoush left Libya and flew to Türkiye on a government plane with the assistance of the Internal Security Agency (ISA), Israel's Ynet said citing sources.
However, ISA denied alleged reports regarding permitting or facilitating her escape, stressing that she did not pass through the official channels at Mitiga Airport.
Mangoush was suspended from her post on Sunday and was referred for investigation after Israel said its Foreign Minister Eli Cohen had met her last week despite the countries not having formal relations.
Libya's Foreign Ministry said Mangoush had rejected a meeting with representatives of Israel and that what had occurred was "an unprepared, casual encounter during a meeting at Italy's Foreign Affairs Ministry."
"I spoke with the foreign minister about the great potential for the two countries from their relations," Israel's Cohen said in a statement.
Cohen said he had spoken to Mangoush about the importance of preserving Jewish heritage in Libya.