A senior army source in Conakry confirmed to the BBC there had been trouble at the camp in Kissidougou but said only one recruit had died.
They had gone on the rampage on Tuesday demanding to be formally enrolled after spending two years in training.
They had enlisted under the junta that handed over after elections last year.
Instructors fled, along with civilians from the immediate surroundings.
Eyewitnesses say when reinforcements later arrived from nearby garrison towns to quell the trouble, there were deadly confrontations between the recruits and soldiers.
The military junta headed by Capt Moussa Dadis Camara seized power in 2008 on the death of long-time leader Lansana Conte.
A year later, Capt Camara went into exile after an assassination attempt and his deputy oversaw the handover to civilian rule.
The BBC’s Alhassan Sillah in Conakry says it is not the first time that young recruits associated with Capt Camara have suffered at the hands of regular soldiers.
After the assassination attempt, some army recruits at a camp west of the capital mutinied and suffered heavy, though unspecified, losses, our reporter says.
Last year’s polls were Guinea’s first democratic election in 52 years.