Military sources and medics said that at least 36 died when loyalists of former general Khalifa Haftar and regular army troops attacked militiamen in east and south Benghazi.
The pro-government forces recaptured military positions that the militants, including the radical Ansar al-Sharia group, had seized in July, the military sources said.
A spokesman for Libya's special forces said the unit took back its headquarters on the road to Benghazi airport, in the city's southeastern Bouatni region, Al Jazeera reported.
Armed forces general staff spokesman Colonel Ahmed al-Mesmari said the entire east of Benghazi was now back under the control of government troops, while pro-government forces were making advances in the south of the city.
Air strikes targeted several neighborhoods, including the militant stronghold of Al-Gawarsha in the west, witnesses said.
They said the government troops had been deployed in several parts of the eastern city for the first time since July.
Militant groups, including Ansar al-Sharia which is blacklisted by Washington as a terrorist group, have held sway in most of Benghazi since July.