Despite the sound of military helicopters and sporadic shooting heard in Conakry, Cherif said the "the situation is under control".
Those who "orchestrated this insurrection will be punished", he said, adding that Diakite "has been found".
Witnesses said Conakry appeared calm after the incident in the early evening, with hardly any traffic on the streets.
Earlier, residents and tourists near Camp Koundara said they heard repeated volleys of gunfire in the worst unrest since a September 28 crackdown on pro-democracy protesters that rights groups said killed more than 150 people.
Al Jazeera's Yvonne Ndege, reporting from Nairobi, said some sort of dispute had apparently broken out between Camara and Diakite over whether Diakite would be arrested over the September 28 massacre.
Diakite is accused of having led the presidential guard that opened fire on protesters gathered inside the national stadium.
Thursday's shooting underscores the deep rifts within the military which took control of the nation of 10 million on Africa's western coast 11 months ago.
Camara had initially promised to quickly organise elections, but later said he planned to run for office himself in presidential elections scheduled for January 10, prompting the peaceful rally in September.
The government has denied all wrongdoing and blamed opposition leaders for going ahead with the banned protest.
The September massacre led the European Union and the African Union to impose sanctions on Guinea including weapons embargoes, visa bans and freezes on foreign bank assets.
Thursday's incident happened as international investigators were in Guinea carrying out a UN-backed inquiry into the September killings to determine who gave the order to kill.
One diplomat in the city said: "What we are hearing is that they either arrested [Diakite] or were going to arrest him and he shot at [Camara]. There is no doubt that this is linked to the investigation."
Diakite, as well as Camara and several others, may face charges of crimes against humanity by the International Criminal Court.