"The chief of staff presented his resignation that was accepted by the congress," GNC member Abdullah al-Gmati said, adding that the assembly had already been preparing a vote to suspend Mangoush.
His resignation was approved by a vote in the GNC, another member of the congress said.
Gmati also said that the GNC has given the government two weeks to put into place a plan to dissolve armed groups and integrate their members individually into the regular security forces.
Clashes erupted yesterday after dozens of demonstrators, some of them armed, tried to force the powerful "Shield of Libya" brigade from its Benghazi barracks, an AFP correspondent reported.
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They encircled the headquarters and called on regular security forces to step in, saying they wanted rid of armed militias in the city.
The "Shield of Libya" is mostly made up of rebels who battled dictator Muammar Gaddafi in 2011, and is formally under defence ministry control.
In May, the GNC had already decided to replace Mangoush, but said it had yet to decide on criteria for his replacement.