Government aides said a landmine caused the explosion, which sharply raised tensions in a city controlled largely controlled by Gedi's political foes.
One government source said unidentified attackers had thrown a hand grenade under Gedi's car as it passed seconds before the landmine blast in an apparently co-ordinated attack.
The blast set ablaze at least one vehicle among several that were ferrying Gedi and one of his deputies from an airstrip to the lawless Indian Ocean city.
"Five seconds after the blast, there was an exchange of fire, I don't know who between," a wounded man who had been riding in the convoy told Reuters from his hospital bed.
"The tyres on our car were shredded by bullets."
Gedi had flown in from his headquarters north of the capital to try to hold talks with a dissident faction of ministers based in Mogadishu to end a rift in the government that has stirred fears of renewed civil war in the chaotic Horn of Africa nation.
Six people were killed in the blast, the medical sources said, and a government source said four of the six had been burnt beyond recognition. About 20 were wounded.
"It struck the car directly behind the prime minister's car, and that vehicle burst into flames," Ali Nur Sahal, an aide to Deputy Prime Minister Hussein Aideed, told Reuters.
"We believe it was a landmine."
Aideed, also Interior Minister, had welcomed Gedi at the airstrip and was also in the convoy. He too was unhurt.