The federal Somali government signed the terms of an agreement in Ethiopia with southern political leaders to set the terms of government for Lower Jubba, Middle Jubba and Gedo in the south of the country.
Nicholas Kay, U.N. special envoy to Somalia, said the decision was a step in the right direction for the federal republic.
"This is a significant step towards restoring peace in Somalia, building a strong Federal Somalia and contributing to regional and international security," he said in a statement Wednesday. "This agreement unlocks the door to a better future for Somalia."
Somalia last year established its first formal central government since 1991. The country has struggled to consolidate gains because of separatist campaigns and terrorist activity tied to al-Qaida affiliate al-Shabaab.
Doctors Without Borders announced it was ending its mission in Somalia because of attacks against healthcare workers.
Kay said gains made in Somalia are "reversible" if the international community takes its focus off the country.