The soldiers fired their guns into the air from their barracks in the capital, Conakry, and the western town of Kindia, the central town of Labe and the southeastern town of Gueckedou near the border with Liberia, reports said.
Sources at Donka Hospital in Conakry said about nine people had been treated for gunshot wounds sustained from stray bullets.
"The Guinean security forces have a history of acting with utter disregard for Guinea's citizens," said Corinne Dufka, senior West Africa researcher for New York-based Human Rights Watch. "Ending impunity and making the armed forces accountable for their behaviour is a key test for the new government."
A new government, led by consensus Prime Minister Lansana Kouyate, was established following massive strike-led protests in January and February. The unrest left at least 129 people dead after the military intervened to quash the demonstrations.
Efforts are underway to establish an independent commission to investigate abuses allegedly committed by the military during the protests. At around that time, soldiers had received promotions and pay hikes.
Soldiers angry over President Lansana Conte's rejection of demands for pay rises staged a two-day violent mutiny in Conakry in 1996. They seized the country's international airport, bombed the presidential palace and engaged in widespread looting. Dozens of people were killed. The mutiny ended after Conte promised to increase the soldiers' salaries.
Conte, an ailing former general, seized power in 1984 and has been heavily relying on the military's support through out his 23-year rule.
Sources close to the soldiers protesting on Wednesday and Thursday say the mostly low-ranking troops want the government to give them 300-billion Guinean francs [US$82 million] Conte allegedly promised them to end the 1996 mutiny.