Sidiki Diakate, a senior official in the ministry of health, said: "Of the 49 killed, 34 were in Conakry [the capital] and 15 in the provinces."
The government announcement came as demonstrations calling for Conte to resign continued across the country on Thursday for the sixteenth consecutive day of a strike aimed at ousting the president.
Conte, Guinea's long-time head of state, had on Wednesday agreed in principle to name a consensus prime minister, one of the protesters' main demands.
After this concession by the government, talks restarted late on Thursday between representatives of Conte's regime and the trade unions that have organised the strike.
But despite the fresh attempt at dialogue between the government and the strikers, new protests broke out in parts of the country as demonstrators renewed their demands that Conte resign, police said.
About 15,000 demonstrators took to the streets of the main administrative centre of Kankan, in the east of the country, urging union leaders to beware of "cunning" by the 72-year-old president, who has ruled since 1984.
Hundreds of other demonstrators gathered in central Labe and Yimberin in the north, police and witnesses said.
In Conakry, the capital, there were fewer police and troops on the streets than on Monday, the bloodiest day of the strike, when security forces fired at demonstrators during running battles.
The 59 deaths resulting from the violence have provoked international criticism.