The developments underlined the security chaos in Libya more than a year and a half after longtime dictator Muammar Gaddafi was deposed in a civil war.
The violence broke out yesterday when protesters stormed a base belonging to Libya Shield, a grouping of militias aligned with the military that were tasked with helping to maintain security. The protesters were demanding that the militias leave their camp and submit to the full authority of Libya's security forces.
Witnesses said some of the protesters brought weapons to the camp, which was the main Benghazi base for Libya Shield militiamen. The militiamen appeared outnumbered by hundreds of protesters outside the gates.
Hospital officials said protesters made up most of the dead. Many were buried today. The officials spoke anonymously as they were not authorised to speak to reporters.
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According to the director at the city's Jalaa Hospital Mohamed Belied, the deaths were caused by gunshots and explosive fragments. He said that dozens of people were wounded.
Military officers had been protesting against al-Mangoush for weeks, accusing him of corruption and of failing to exert authority over militias. Some militias were believed to have favoured al-Mangoush remaining in his post, because he had been unable to replace them with a strong unified force.
Benghazi, the birthplace of the revolution that led to the ouster of Gaddafi, was the site of the September 11 assault last year on the US diplomatic mission that killed Ambassador Chris Stevens and three other Americans. High level police officials have also been assassinated and security bases have come under frequent attack there by unidentified assailants.
The deadly clashes are likely to further enflame anger against militias, which have been accused of acting with impunity and enforcing their own agendas.