The leaders gathered at a stadium in southern Mogadishu and handed over dozens of battle wagons - pickup trucks with anti-aircraft artillery or large-calibre machine guns mounted in their wells - and hundreds of machine guns to the country's Deputy Prime Minister Mohamoud Abdullahi Jama.
"This is the beginning of a voluntary disarmament by the Somalis. It is a milestone for the relocation of the Somali government to the capital of Mogadishu," Jama told the men.
The commanders are also ministers in the transitional government exiled in Kenya.
"These are not our weapons any more; they belong to the Somali people," Musa Sudi Yalahow told hundreds of Somalis who attended the ceremony.
It is the first time the leaders are surrendering arms since 1991, when toppling of dictator Mohammed Siad Barre plunged the nation into anarchy, they said.