The operation came as three members of forces loyal to the Tripoli-based Government of National Accord were killed further west in a resumed offensive against Islamic State group holdouts in Sirte.
The GNA is the centrepiece of UN efforts to restore stability in Libya and forge a central authority capable of tackling the twin scourges of IS and rampant people trafficking across the Mediterranean to Europe.
But it has struggled to impose its authority amid opposition from a rival administration based in Libya's remote east. Oil is Libya's key asset, and revenue from crude exports is vital if the GNA is to rebuild an economy and infrastructure ravaged by violence since the 2011 uprising that killed veteran dictator Muammar Gaddafi.
Last week, forces led by controversial military strongman Khalifa Haftar seized Ras Lanuf, Al-Sidra, Zuwaytina and Brega in the so-called "oil crescent" along the coast.
They later handed the ports over to the National Oil Corporation, which said on Thursday that crude exports would resume "immediately" from Zuwaytina and Ras Lanuf.
The NOC says it is loyal to the GNA, but also to the internationally recognised parliament based in the east which supports Haftar's forces and has refused to give the GNA its vote of confidence.
Early Sunday, pro-GNA forces launched an offensive aimed at retaking Al-Sidra and Ras Lanuf, but after several hours of fighting Haftar's forces said they launched a counter-attack and repelled the loyalists.
"We repelled the attack and we are chasing them in the region," said Muftah al-Muqarief, who heads oil guards loyal to Haftar, adding that "some" assailants had been captured.
There was no independent confirmation from the oil crescent region of the fighting and the situation on the ground. A Haftar spokesperson, Mohamad Ibset, said earlier that guards loyal to the GNA had attacked.
Tanker withdrawn for safety And Ali al-Hassi, a spokesperson for the loyalist oil guards, said: "We attacked Al-Sidra and Ras Lanuf, and Haftar's forces are trying to hit us with their warplanes."
The counter-attack is a new blow to the unity government and NOC efforts to resume exports. "We ask the combatants to avoid taking actions that could damage our vital national infrastructure," NOC chairman Mustafa Sanalla said in a statement.
"Our national recovery depends on these ports being open and our oil flowing freely." The NOC said Maltese-flagged tanker the Seadelta, which was due to load crude oil at Ras Lanuf for Italy, had to be "withdrawn to a safe distance offshore" because of the fighting.
Meanwhile firefighters were trying to extinguish a blaze at Al-Sidra, where another storage tank already damaged in January fighting was set alight during Sunday's clashes.
Libya, with Africa's largest oil reserves estimated at 48 billion barrels, has exported only a few tankers of crude in recent months. The GNA, created last year as a UN-brokered power-sharing government, still needs a vote of confidence from the rival parliament based in the east.
Haftar, who sees himself as Libya's saviour after driving jihadists out of most of second city Benghazi, is the most powerful backer of the rival administration in the east.
Days after the ports fell under his control, the east-based parliament promoted him to field marshal from his previous rank of general.
Also on Sunday, pro-GNA forces renewed attacks on IS holdouts in Sirte after a two-week lull.
"Our forces are using heavy artillery to target the positions where Daesh (ISIS) holdouts are cowering," they said in a statement.
A field hospital on the outskirts of Sirte said three members of the loyalist forces were killed on Sunday. More than 450 members of the loyalist forces have been killed and around 2 500 wounded since the operation began in May.
Pro-government forces have said the situation at Misrata Central Hospital where doctors have been overwhelmed by casualties is also delaying the final push in Sirte. Italy has said it will set up a military field hospital in Misrata, following a request from the GNA.