Witnesses said the clashes, which included heavy artillery, were some of the fiercest to hit Benghazi since former general Khalifa Haftar launched a new government-backed offensive on the eastern city in October.
Islamist militias including fighters from the radical Ansar Al-Sharia group took near total control of Benghazi in July.
At least 32 people, including civilians, have been killed in the fighting since Monday, according the Benghazi Medical Centre. It said seven people had been killed on Wednesday alone.
Since the start of Haftar's assault, 286 people have been killed, based on an AFP toll comprised of figures provided by medical and security sources.
Islamist groups do not disclose their death tolls.
Clashes on Wednesday morning focussed on the east, west and centre of the city, especially close to Benghazi's security headquarters, which was retaken from the Islamists two days ago, said Colonel Ahmed al-Mesmari.
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"The army is facing strong resistance from armed Islamists," he added.
The Islamists erected sand bag barricades across the city's main roads and patrolled areas in armed vehicles mounted with anti-aircraft guns, witnesses said.
A security official said Haftar's forces conducted air strikes against the rebels in the city centre.
The area close to Benghazi's port was also the scene of fierce fighting, with pro-government forces looking to wrest control of the strategic hub from the Islamists.
Libyan authorities have struggled to assert control across a country awash with weapons and powerful militias which ousted longtime autocratic leader Moamer Kadhafi in a 2011 revolt.
The internationally recognised government was forced to take refuge in the country's east to escape a mainly Islamist coalition which seized control of Tripoli at the end of August.
France, Britain and the United States on Tuesday asked a Security Council committee to add Ansar al-Sharia to a UN terror list for its ties to Al-Qaeda.