An Islamist and jihadist alliance announced the capture yesterday of the main military base in the eastern city in a statement which was confirmed by an army official.
He said jihadists of Ansar al-Sharia, blacklisted as a terrorist organisation by Washington, were among the groups.
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"Special forces under the command of (Colonel) Wanis Abu Khamada withdrew after several attacks," said the army official after the biggest loss yet for the armed forces in its fight against the country's powerful militias.
The special forces are one of the units of Libya's regular armed forces that support rogue Libyan general Khalifa Haftar but have not placed themselves under his command.
Haftar began his offensive against radical Islamist groups in Benghazi, dubbed "Operation Dignity", in mid-May.
On its Facebook page Ansar al-Sharia published photos of dozens of weapons and crates of ammunition it claimed to have seized.
Former deputy prime minister and newly-elected MP Mustapha Abu Shagur was meanwhile freed by his kidnappers, hours after they snatched him from his Tripoli home, his family said.
The kidnapping highlighted the failure of authorities to rein in dozens of militias that sprang up during the 2011 uprising which overthrew longtime dictator Moamer Kadhafi.
"Doctor Abu Shagur has been freed. He is tired but in good health," his nephew Isam al-Naass told AFP. "He was not treated badly" by his kidnappers, he added.
Shagur would not talk about his ordeal or the identity of his kidnappers.
Amid the increasing lawlessness and uncertainty, France, Portugal, the Netherlands, Canada and Bulgaria became the latest nations to ship out their citizens or close their embassies in Tripoli.
The blaze at the Tripoli fuel depot near the international airport erupted on Sunday when a rocket fired during clashes between rival militias battling for control of Tripoli international airport struck a tank containing more than six million litres of fuel.
It then spread to another fuel storage site nearby.
Authorities warned the fire could spread still wider to a natural gas reservoir, where 90 million litres are stored, amid fears a huge fireball could cause widespread carnage.
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