Guinean Prime Minister Ahmed Tidiane Souare said on Tuesday that his government had not been dissolved, agencies' reports said.
That came after radio broadcast from the Guinean capital of Conakry said a military coup followed the death of the president, forcing the government and the constitution to dissolve.
Souare told state radio that he is still in office with his government continuing its function.
Earlier in the day, a group of men in military uniform appeared at state radio and TV broadcasting stations, making the announcement of the suspension of the constitution and the government.
"From today on, the constitution is suspended, and so are all political and group activities ...the government and republican institutions are dissolved," said Capt. Moussa Camara, spokesman for a self-claimed National Council for Democracy.
Capt Camara said a consultative body composed of civilian and military representatives will soon be created.
"With the immense natural resources it is entitled, Guinea could have been more prosperous, but its history and people decided otherwise," he said, adding "the members of actual government are largely responsible for these unprecedented social and economic crises."
Capt. Camara ordered government officials to report at the Alpha Yaya Diallo barracks, known for army mutinies against Conte when he was in power.
Conte died at the age of 74 at 6:45 p.m. local time (1845 GMT) on Monday in a hospital in Conakry, apparently after having diabetes for long.
He came to power in 1984 and was elected president in 1993. He won re-elections in 1998 and 2003. His death was announced by National Assembly President Aboubacar Sompare, who is to temporarily take over state affairs under the constitution while organizing a presidential election within 60 days.
Souare on state TV announced "a national mourning of 40 days."
By far, the African Union (AU) has condemned the coup in a statement, denouncing it as "a flagrant violation of the constitution and of African legality."
The European Union has issued a call for the respect for " constitutional rules in order to ensure a peaceful transition."
Conte ruled the country for 24 years since seizing power in a military coup in 1984. He was the second president after his predecessor Ahmed Sekou Toure died on March 26, 1984.
Guinea won independence from France in 1958. It borders Guinea- Bissau, Senegal and Mali in the north, Cote d'Ivoire in the east, Sierra Leone and Liberia in the south and the Atlantic Ocean in the west.
With an area of 245,857 square km and the population of 9.56 million, the country is also known for its rich mineral deposits, especially bauxite which accounts for half of the world's total reserves. The country, however, remained one of the poorest in the world.