Mahmoud al Werfalli's killing underscores the risks of violent escalation on the ground that poses the biggest challenge to Libya's new unity government.
Gunmen have assassinated a mid-tier leader of warlord Haftar's – who was wanted by the ICC for war crimes.
Mahmoud al Werfalli was shot on Wednesday from a car outside a hospital in Benghazi alongside two of his bodyguards, military sources said, amid growing friction between rival factions in eastern Libya. They spoke on condition of anonymity because they were not authorised to brief the media.
Al Werfalli’s brother was wounded in the attack, they said.
The International Criminal Court (ICC) in The Hague has indicted Werfalli twice for the suspected killing of more than 40 captives, including in a 2018 incident in which photographs appeared to show him shooting 10 blindfolded prisoners.
This month he was shown in a widely circulated video raiding a car showroom in Benghazi alongside his uniformed men, smashing up furniture and computers as they brandished weapons.
In December 2019, the US Treasury included Al Werfalli on its sanctions list, accusing him of committing serious human rights violations.
No group immediately claimed responsibility for the attack that comes after a transitional government took power last week with the job of leading the country out of years of war and to elections, scheduled for December.
Following the attack, there was a heightened presence of security forces in Benghazi, with residents across the city saying they heard gun shots.
Friction between rival factions in eastern Libya has been escalating for some time and could further degenerate into a series of retaliatory attacks, said Tarek Megerisi of the European Council on Foreign Relations.
"I think this is going to be the first major challenge for the (Government of National Unity) GNU," he said.
Besides the challenge of merging Libya's divided state institutions and preparing for elections in December, the GNU needs also to tackle a dire security situation with power held by myriad factions.
On Wednesday, UN Special Envoy Jan Kubis told the Security Council: "Various armed groups continue to operate without hindrance, human rights violations continue with almost total impunity."
Last week, GNU Prime Minister Abdelhamid Dbeibeh said his government would open an investigation after the discovery of bodies in Benghazi.
Since 2011 US-led toplling of the Gaddafi regime, Libya has descended into chaos and has become a haven for armed groups.
The North African country has not brought any suspects before the International Criminal Court in the 10 years since it was referred to the ICC by the UN Security Council.
The allegations have centered on suspected crimes committed either during the 2011 uprising that ousted and killed longtime dictator Moammar Gaddafi, or the civil war that followed.
Others wanted by the ICC are Seif al Islam Gadhafi, the late dictator’s son, as well as Al Tuhamy Mohamed Khaled, former head of Libya’s Internal Security Agency.