"The ambassador and more than 50 staff and diplomats of the Egyptian embassy left Tripoli on Saturday evening," ministry spokesman Saeed Lassoued told AFP.
The evacuation had been decided on security grounds, he said, as Libyan authorities worked to secure the release of the abducted diplomats.
Justice Minister Salah al-Marghani has implicitly linked the kidnappings to the arrest in Egypt on Friday of a prominent former Libyan rebel commander who fought in the 2011 uprising against Muammer Gaddafi.
"We await an explanation from our Egyptian brothers on the accusations against Shaaban Hadeia," Marghani said late Saturday, while condemning the kidnappings as a "criminal act".
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The foreign ministry, meanwhile, said it was in contact with Cairo requesting information on Hadeia and seeking his early release.
Kidnappers seized Egypt's cultural attache and three other embassy staff yesterday, a day after a group snatched another Egyptian official in the city.
Egypt's foreign ministry spokesman Badr Abdelatty has confirmed Hadeia was detained in Egypt.
Abdelatty said the embassy in Tripoli was being evacuated as a "temporary precautionary measure".
With growing insecurity in post-revolt Libya, authorities have struggled to integrate rebel groups which helped topple Gaddafi into the regular security forces.
Some militias have carved out their own fiefdoms, each with its own ideology and regional allegiances.