The government of President Lansana Conte blamed the opposition for stirring violence during the student protests against the suspension of exams due on Monday in the former French colony.
"A lack of control resulted in the loss of life and important material damage both in (the capital) Conakry and in certain towns in the interior," Moussa Solano, a government spokesman told state media, without providing further details.
Three people were killed in Conakry, including a child hit by a stray bullet, when an isolated soldier opened fire after being mobbed by angry students, a police source said.
A further three died in the eastern town of Nzerekore, some 970km southeast of Conakry, after troops shot at a demonstration against the government.
It was the second day of violent student protests in the West African country.
A riot broke out in the provincial capital after students began to taunt police when it became clear that adjudicators for Monday's exams had not turned up, despite government reassurances the nationwide tests would go ahead.
In another Conakry neighbourhood students shouting "Down with the government" ransacked local education offices and rampaged through the streets, despite police efforts to contain them.