Military spokesman Mohammad al-Azumi said Haftar's forces were able to take control of Zuwaytina port and secure it completely on Monday.
The fighters, who support the rival government based in east Libya, had seized two other Mediterranean oil ports of al-Sidra and Ras Lanuf on Sunday, according to Azumi.
"The armed forces are now concentrated at the port and have secured it after expelling outlaw militia from it," the LANA news agency reported.
Another spokesman of Haftar's forces said efforts were underway to seize the port of Brega, that remains in the hands of GNA guards.
The GNA government has called on its forces to "protect and defend" the ports against what it describes as "flagrant aggression" against the county’s sovereignty. The oil ports are considered as a vital source of income for the government.
This was reportedly the first time that the rival administration's forces and fighters loyal to the UN-backed government clashed directly.
The North African country has had two rival governments since mid-2014, when militants overran the capital and forced the parliament to flee to the country’s remote east.
The two governments reached a consensus on the formation of the GNA in December 2015, after months of UN-brokered talks in Tunisia and Morocco to restore order to the country. Libya, however, continues to be gripped by political strife and violence.
Libya has been the scene of increasing violence since 2011, when long-time dictator Muammar Gadhafi was toppled from power after a NATO military intervention. His ouster created a huge power vacuum in Libya, leading to chaos and emergence of numerous militant groups.
Since then, the country has been wracked by violence, with the rival administrations and their allied militias battling for power.
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