But Youssouf Bah, a Guinean journalist, told Al Jazeera that Camara had been shot in the head. Guinea's communication minister denied that the de facto president had received any head injuries.
Camara arrived at a Moroccan military airport on Friday and is expected to receive medical treatment, government officials told Reuters.
Officials identified Aboubacar Toumba Diakite, the head of the presidential guard and a close aide to Camara, as having opened fire on the president during a visit to a military camp in Conakry.
Those who "orchestrated this insurrection will be punished", Idrissa Cherif, Guinea's communications minister said on Thursday, adding that Diakite "has been found".
But later reports said Diakite had gone into hiding.
"He is in a safe house," a source in Diakite's entourage said, and a military official confirmed the report.
The attack came as UN investigators in Conakry wound up an inquiry into a bloody crackdown by security forces on pro-democracy protesters gathered inside the capital's national stadium.
Diakite is accused of being the leading figure in the September 28 incident in which more than 150 people were killed and scores of women raped, according to witnesses.
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 in connection with the massacre.
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.
The assassination attempt 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.