A spokesman for east Libyan armed forces said on Friday that as many as 141 people had been killed a day earlier in an attack on a southern air base.
The head of Libya’s United Nations-backed government suspended his defence minister pending an investigation into the incident.
The attack at Brak Al-Shati air base shattered a truce in the area, which in recent months had become a flashpoint between military alliances based in eastern and western Libya.
It risks a major escalation in a stop-start conflict between eastern-based factions and rivals loosely aligned with current and former governments in the capital, Tripoli.
Ahmed al-Mismari, a spokesman for the eastern-based Libyan National Army (LNA), said 103 of those killed in the attack at the air base were LNA troops, most of them from the 12th Brigade stationed there.
They were attacked by a brigade from the western city of Misrata known as the Third Force, which previously controlled the base and is nominally aligned with the UN-backed Government of National Accord (GNA) in Tripoli.
Earlier on Friday, the mayor of Brak Al-Shati and a medical source in the town put the death toll at 89, though the medical official said some bodies had not been brought to the hospital. Mr Mismari said some of the bodies were only collected on Friday.
It was not possible to independently verify the number of casualties. Local and LNA officials have said some of those killed were civilians who appeared to have been summarily executed. Mohamed Gliwan, a spokesman for the Third Force, told local TV that LNA troops who were killed inside the base were armed.
Human Rights Watch cited a medical official, an eyewitness, and photo and video footage to say that attacking forces had killed "scores of LNA fighters, some with bullets to the head, in apparent acts of summary execution". UN Libya envoy Martin Kobler called the attack unprovoked and vicious, saying it "must not push (Libya) into further, serious conflict."
GNA prime minister Fayez al-Sarraj announced that he was suspending both defence minister Mahdi Al-Barghathi and Third Force commander Jamal Traiki, "until it is determined who was responsible for violating the ceasefire".
He condemned the escalation at Brak Al-Shati “in the strongest terms” and called for an immediate ceasefire. He denied issuing any instructions to the ministry of defence.
Mr Barghathi is a former LNA commander turned opponent of LNA chief Khalifa Haftar.
Also on Friday, a car bomb south of Benghazi killed a prominent tribal leader linked to the LNA along with five other people. The blast in Suluq, 50km (31 miles) south of Benghazi, also wounded 26 people, a medical source said.
The LNA has been fighting a three-year campaign against Islamist militants and other opponents in Benghazi and other parts of eastern Libya.