Police have used rubber bullets and tear gas against protesters in the capital Sarajevo and the northern town of Tuzla.
Black smoke could be seen gushing from the presidency building in Sarajevo.
The protesters are unhappy about the lack of economic and political progress in the Balkan country.
About 40% of Bosnians are unemployed. The unrest is the worst since the end of the Bosnian war.
At least 100 people have been injured in Friday’s protests in the capital.
Sarajevo-based newspaper Dnevni Avaaz says that police used water to disperse protesters who were throwing stones at the presidency building.
On Thursday, clashes between police and demonstrators in Tuzla injured more than 130 people, mostly police officers.
The unrest began in Tuzla earlier in the week, with protests over the closure and sale of factories which had employed most of the local population.
Demonstrators in other towns, including Mostar, Zenica and Bihac, supported the Tuzla workers and criticized the government for failing to tackle the rampant unemployment.
Hundreds of people also gathered in support in the Bosnian Serb capital, Banja Luka.
Local media are reporting that the premiers of two of Bosnia’s cantons – Sead Causevic of Tuzla canton and Munib Husejnagic of Zenica-Doboj canton – are to resign.
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