An initial toll from the Al-Jala hospital in the eastern city said seven people died and 30 were wounded.
An army spokesman in Benghazi, cited by official news agency Lana, confirmed 11 people died but said that only 38 were wounded.
Fighting erupted after dozens of demonstrators, some of them armed, tried to dislodge the powerful "Shield of Libya" brigade from its barracks in Benghazi, said an AFP correspondent at the scene.
Libya's post-Gaddafi authorities, who have still not managed to form a professional new army and police corps, often call on the "Shield of Libya" to intervene in the various tribal conflicts that trouble the country.
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Adel Tarhuni, spokesman for the "Shield of Libya", said one member of the brigade had died and another seven were wounded.
Tarhuni also defended the "legitimacy" of the brigade, saying it officially came under the umbrella of the defence ministry.
He reported that there was a peaceful demonstration in front of the brigade's headquarters, before "armed men" infiltrated it.
Armed forces spokesman Colonel Ali al-Shikhi told Lana the brigade was "a reserve force of the Libyan army," and that an attack on them was equivalent to an "attack on the legitimate authorities."
Shikhi said the incident was "very serious," and called on restraint from all parties.
In October, people in Benghazi managed to force other militias from their bases.