An alliance of militant groups announced capture of the main military base in the eastern city in a statement which was confirmed by an army official.
He said militants of Ansar al-Sharia were among the groups. The group has been blacklisted as a terrorist organisation by Washington.
Intense fighting in Benghazi for the past week has claimed about 60 lives since Saturday, medics said.
“Special forces 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.
Ansar al-Sharia, on its Facebook page, displayed photos of dozens of weapons and crates of ammunition it claimed to have seized.