The loss comes after fighters backing a rival administration in east Libya seized two other terminals from guards loyal to the Tripoli-based Government of National Accord (GNA) yesterday.
All three Mediterranean ports are in Libya's "oil crescent", an area seen as a vital source of income for the GNA, which has struggled to assert its authority across the country.
"Our armed forces were able to take control of Zuwaytina port and secure it completely," a spokesman for the fighters that took the terminals said.
The forces are commanded by controversial general Khalifa Haftar, who has refused to back the GNA and supports the parallel authority based in east Libya.
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Yesterday they took the Al-Sidra and Ras Lanuf ports before attacking Zuwaytina to the east.
It is the first time that Haftar's forces and fighters loyal to the GNA have clashed directly since the unity government started working in the capital in March.
It warned overnight that the country was at a "critical juncture", adding "the hopes of Libyans for stability in the country have been dashed".
The head of the rival government in the eastern city of Bayda said it would work on reopening the ports as soon as possible.
"We will work on the oil ports resuming work as soon as possible so as to guarantee all Libyans a decent life," Abdullah al-Thani said.
Haftar's forces said they would hand over the management of the ports to the National Oil Corporation (NOC) to resume oil exports.
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