Lt Diakite (r) is accused of trying to shoot dead Capt Camara (l)
Guinea's military leader, Capt Moussa Dadis Camara, has arrived in Morocco for medical treatment after being shot by an aide on Thursday, officials say.
He has been rushed to the Hay Riyad military hospital on the outskirts of Rabat, reports Reuters news agency.
Guinean officials insist Capt Camara is able to walk and talk but some sources say he has a serious head wound.
This is believed to be the first time Capt Camara has left the country since seizing power last December.
Analysts say he may fear being toppled in his absence and so his departure indicates his condition may be serious.
But this was denied by government minister Keletigui Faro.
By Mark Doyle, BBC News, recently in Guinea
It appears that what happened on Thursday night is that Capt Dadis Camara travelled from his stronghold in one military camp on the outskirts of Conakry to meet Lt Aboubacar Diakite, known as "Toumba", at another military camp in the centre of the city.
A firefight then broke out between the forces of the two men. Reports say Capt Camara was injured, and then, with helicopter support, was evacuated from the area. What is not yet known is why the leader of the junta decided to confront Toumba at this time.
Tensions have been high since late September when soldiers massacred scores of pro-democracy activists who were demonstrating at a rally in a football stadium.
A UN commission of enquiry is currently in Guinea trying to establish which soldiers were responsible. Diplomats say Toumba was present at the stadium when the killings took place - but so were other officers who remained loyal to Captain Dadis.
"His condition is not very serious but he'll need to undergo extensive medical tests in Morocco," he told the BBC French service for Africa.
"No bullet penetrated the president's body. There was just a graze on the head. He is walking normally and speaking with people," said Communications Minister Idrissa Cherif, Reuters reports.
Morocco has said it will treat Capt Camara for humanitarian reasons, even though it had not been informed of his arrival.
He has not been seen in public or appeared on national TV or radio since the shooting.
A Senegalese medical team flew to Guinea to treat him on Thursday night.
Maj Faro said that Aboubacar "Toumba" Diakite, the officer who allegedly tried to kill Capt Camara, and his former aide-de-camp, has gone into hiding.
Road-blocks have been set up on the two main roads into Conakry by security forces trying to find him.
Analysts say the shooting highlights deep rifts within the junta after the killing of an estimated 157 opposition supporters in September.
BBC West Africa correspondent Caspar Leighton says the presence of a UN investigation team in Conakry this week has heightened concerns among some parts of the military that they may be singled out by the government to take the blame for the attack.
CAPT MOUSSA DADIS CAMARA
Born 1964 in far south-east
Seized power in December 2008 as a little-known army captain
Promised democracy but then showed signs of holding onto power
Increasingly erratic behaviour and public humiliation of officials
Has pledged to tackle drugs traffickers
Initially blamed "uncontrollable" military elements for September 28 killings
Lt Diakite has been accused by witnesses and human rights groups of commanding the troops who carried out the massacre. Several women have reported being gang-raped by soldiers.
The military authorities insist that 58 people died, most of whom were trampled to death, not shot.
Capt Camara was at first popular when he seized power after years of autocratic rule and promised not to remain in power.
However, that has changed since he appeared to renege on that promise and hinted that he might stand in elections scheduled for January.
This culminated in the massive protest on 28 September and the brutal crackdown.
Arms embargoes and travel restrictions have been imposed against the junta by the European Union and West African alliance Ecowas.
The EU has called for Capt Camara to be tried for crimes against humanity, while the African Union has been urging him to stand down.