Kenyan forces will hand over control of the Kismayu port and airport to the Somalia government.
In a joint communiqué issued by regional leaders meeting in Kampala on Sunday, they resolved to end the long running dispute over control of the two facilities by handing them over to Somalis.
The resolution follows a long running dispute for the facility between the government of Somalia and the Kenya Defence Forces.
The leaders also banned Somalia from exporting charcoal to Asia with immediate effect.
Sources at the meeting told the Daily Monitor that Somali Deputy Prime Minister Fowzio Aden accused Kenya of meddling in the affairs of Kismayu leading to fights between two rival groups.
But Uganda Foreign Affairs minister Sam Kutesa denied the issue had been discussed.
“Amisom is doing well and there are no such allegations,” he said.
The Kampala meeting was attended by Presidents Museveni, (Uganda), Uhuru Kenyatta (Kenya), Sheik Hassan Sheik Mahmood (Somalia ), Ethiopian Prime Minister Hailemariam Desalegn and Mr Andrew Bagali who represented Sierra Leone.
Meanwhile, African Union mission in Somalia wants the number of peacekeepers increased from 17,730 to over 20,000.
Mr Kutesa told Journalists in Munyonyo on Saturday that the current African Union force is overstretched.
The creation of zonal forces, Mr Kutesa said would exert pressure on Al-Shabaab fighters who have changed tack after losing most of their main bases in Somalia to African Union forces.
“The force is smaller and overstretched because the area under Amisom is expanding,” he said. Uganda, which was the first country to deploy troops in Somalia in 2007, has the highest number of troops.