Youths stormed and ransacked the building housing the Brotherhood, after hundreds took to the streets overnight to denounce the assassination of Abdessalem al-Mesmari, an anti-Islamist lawyer who campaigned for a civil state.
The demonstrators accuse the Brotherhood of being behind killings that have targeted dozens of officers, especially in Benghazi, cradle of the 2011 armed uprising that ousted dictator Moamer Kadhafi.
In Tripoli, hundreds of people had gathered on Saturday morning at Martyrs' Square, in the heart of the capital, for a demonstration in "solidarity with Benghazi" and against the Islamist movement.
About 100 youths descended on the offices of the Brotherhood-backed Party of Justice and Construction, smashing its windows and looting its furniture.
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Mesmari was shot dead as he left a mosque in Benghazi while an army and a police officer were killed in separate attacks in the restive city on Friday, a security official said.
The prominent activist was among the first Libyans who launched the 2011 uprising against Kadhafi. He helped found the political wing of rebels who later overthrew the regime.
Since Kadhafi's fall, eastern Libyan has been hit by bombings and a series of assassinations and attacks against judges, military and police officers who served under the Kadhafi regime.
Attacks have also been carried out against Western interests.
On September 11 last year, Islamist militants attacked the US consulate in Benghazi, killing ambassador Chris Stevens and three other Americans.