It takes the total exhumed in recent months to 112.
The graves are located in Tarhuna, where eastern strongman Khalifa Haftar’s forces launched an aborted assault last year on the capital Tripoli.
The area, some 80 kilometres (50 miles) southeast of Tripoli, served as the main staging point for Haftar’s failed offensive.
The presence of mass graves in Tarhuna was first reported after the withdrawal of Haftar’s forces from western Libya in June.
Libya’s GNA Interior Minister Fathi Bashagha said the graves represented “atrocious acts” that cannot go “unpunished”.
Bashagha said one of the bodies exhumed was Mabrouk Khalaf, a general and former director of information.
Libya, with Africa’s largest proven crude oil reserves, has been wracked by conflict for nearly a decade, since the overthrow and killing of dictator Mouammar Kadhafi in a NATO-backed uprising in 2011.
It has since been dominated by armed groups and divided between two administrations that have long been bitterly-opposed: the GNA in Tripoli and a rival administration in the east backed by Haftar.
The warring factions signed a “permanent ceasefire” last month after UN-sponsored talks in Geneva.