One doctor, who did not want to be named, told AFP news agency there were “bodies lined up as far as the eye can see in the hospital”.
“Others are lying on the floor in the hallways. The morgue is full,” he added.
Local media said police had used tear gas after supporters of the visiting team, Labé, threw stones towards the pitch in anger at the referee.
“It all started with a contested decision by the referee. Then fans invaded the pitch,” one witness told AFP.
Videos and images on social media verified by the BBC show chaotic scenes outside the stadium, with large crowds attempting to climb over walls and numerous bodies on the ground.
Some of those lying unresponsive on the ground appear to be children.
Paul Sakouvogi, a local journalist in Nzérékoré, told the BBC that the stadium had been “packed to the rafters” with thousands of people.
“There was only one exit… some people climbed over the walls to get out and in the panic, all the spectators headed for the exit, which was very small. Those who couldn’t hold on ended up on the floor,” Mr Sakouvogi said.
He added that internet access in the region had been restricted, and that police were guarding the entrance to the hospital where the injured were being treated.
“I observed six police pick-ups positioned in front of the three entrances to the hospital. They allowed only the medical staff to access the hospital, while the others were told to go back the way they came,” he said.
Prime Minister Bah has paid tribute to the dozens of people killed and promised full medical and psychological support to all those injured.
Guinea’s football body, Feguifoot, has called it a moment of “intense pain” and said that football is meant to “unite hearts and bring minds closer” not cause “tragedy and grief”.
“May the souls of the departed rest in eternal peace,” said the Confederation of African Football (Caf) in a statement from its president, Patrice Motsepe.
Guinea is one of several countries – including Ethiopia, Gambia, Chad, Sierra Leone – that are currently banned from holding international football matches because Caf says its venues do not meet international standards.
That meant that when Guinea took part in recent Africa Cup of Nations qualifiers, all their home matches had to be held in neighbouring Ivory Coast.
According to Mr Sakouvogi, the stadium in which Sunday’s crush occurred is an unfinished project that was started decades ago.