Marghani told the BBC that staff members from the Justice and Foreign Ministries were able to return to their offices last weekend after gunmen ended their siege.
Gunmen took over government buildings demanding that officials who served under Moammar Gadhafi be removed from their posts. Lawmakers recently passed legislation that would prohibit Gadhafi-era officials from government positions.
"We hope this does not happen again and that lessons have been learned that state institutions should not be touched," Marghani said.
The post-war government in Libya has struggled to exert authority over the entire country. Libyan Defense Minister Mohammed al-Bargathi protested last week that the government was under the influence of armed gangs.
Last week, the U.S. State Department and British Foreign and Commonwealth Office said the threat level for parts of Libya was high. Some embassies had pulled their staff from the country as a security precaution.
The BBC reports that about 1,000 people demonstrated in front of Foreign Ministry building last week. They dispersed after they were beaten by unknown gunmen.