Libyan military forces loyal to a retired general attacked militants in Benghazi on Friday.
Hospital officials say at least 13 people were killed and 100 wounded in fierce fighting in eastern Libya.
Libyan military forces loyal to retired General Halifa Hafter fought battles against the Islamist group Ansar al Shariah and other Islamist militias in the city of Benghazi.
Libyan state television showed black smoke rising over Benghazi after government warplanes attacked Islamist militia bases. The report said the targets were bases belonging to Ansar al Shariah and two other Islamist militant groups.
Al Arabiya TV reported that several thousand members of Libya's army, navy and air force joined General Hafter, a former army chief of staff, in Friday's military operation.
Benghazi is a stronghold of militias with roots in the rebel brigades that toppled long-time Libyan dictator Moammar Gadhafi in 2011.
The U.S. ambassador and three other Americans were killed in Benghazi in September 2012 during an assault by militants on the U.S. consulate.
The report said the targets were bases belonging to Ansar al Shariah and two other Islamist militant groups - the February 17th Brigade and the Rafalah Sahaty Brigade.
Libya's interim prime minister, Abdallah Thani, resigned last month, but is still leading the government in a caretaker capacity.
Speaking to reporters after the airstrike, he said all sides - Islamist militias and government military units - must refrain from violence and obey orders from Libya's official military command structure.
Thani said that incidents such as the clashes in Benghazi are preventing the government from restoring order and putting a stop to crime and terrorism there.
He called on militia leaders to follow orders from the army's chief of staff, and urged all military units and police to oppose outside forces trying to enter Benghazi.
The prime minister did not mention the general by name, but warned the Libyan military to disregard orders from anyone involved in what he called a coup attempt.
The current Libyan army chief of staff, Abdessalem Jadallah, denied that any government forces were fighting in Benghazi.
Jadallah, who is reported to have ties to an Islamist militia himself, told Libyan state TV that “revolutionary forces” - presumably forces loyal to him - to “oppose outside fighters trying to seize Benghazi.”
Hafter's supporters, including Colonel Mohamed Hijazi, told Libyan TV that those in the military who oppose the activities of Islamist militias are trying to restore order to their country:
Hijazi said his men "are defending the nation against extremist Islamist militias." He said the militias have been "setting off car bombs and killing and massacring (innocent people) in the name of religion."
Hijazi said Islamist militias already are in control of portions of Libyan territory including Darnah (or Derna), a port city east of Benghazi.
Libyan TV reported a top general from the government air force also joined the renegade military operation in Benghazi, using air bases in Tobruk and Drina for bombing runs aimed at militants in Benghazi, Baida, Merja, Sahat and Soussa.
Thani, however, insisted that only “one government warplane ... disobeyed orders” and took part in the operation.
Unruly militias control large swathes of Libya, provoking sporadic outbursts of violence, chaos and insecurity.
Government officials, military commanders, foreign diplomats, businessmen and workers have been attacked, kidnapped and sometimes killed. Jordan's ambassador, held by kidnappers for nearly a month, was released earlier this week.
In a related development, Reuters reported Friday that “protesters” took control of several oil ports in eastern Libya.
Separatists belonging to the self-styled “Regional Government of Barqa” recently returned several ports to government control after a lengthy dispute over oil revenues.