The President claimed that the clashes were part of an attempted coup against his rule, and accused the government of being passive and corrupt.
The violence erupted on Thursday night, when special forces raided the home of an opposition minister who was under investigation for corruption, and arrested him.
The next day, National Guard soldiers stormed the special forces headquarters and freed the minister, sparking a gunfight that lasted for hours.
President Embalo blamed the parliament for defending corrupt officials and failing to exercise their oversight role. He said he would appoint a new Prime Minister and cabinet soon.
Guinea Bissau, a small West African nation of about two million people, has a history of political instability and military coups since gaining independence from Portugal in 1974.
--ChannelAfrica/Reuters--