The leaders of Hirshabelle, Puntland, Jubbaland, Galmudug and South-West  are meeting in Baidoa for the second inter- state conference, Radio Dalsan reports.
The diplomatic spate between United Arab Emirates and Somalia is expected to top the agenda.
The ongoing floods that have displaced thousands of people along the Juba and Shabelle rivers and security is expected to be discussed.
As the leaders met President Mohamed Abdullahi Farmaajo started a two day state visit to Qatar.
Last week Jubbaland President Ahmed Islam Madoobe accused Farmaajo of sidelining with Qatar at the expense of Emirati relations.
Madoobe and his Puntland counterpart Abdiweli Gaas had recently paid visits to the UAE.
Gaas told reporters in Abu Dhabi that Puntland had the constitutional right to make deal with UAE .
Somalia assumed a “neutral” stance in the wake of the Gulf Crisis despite a majority Muslim and Arab League nations severing ties with Qatar.
The first inter-state leaders conference was held in Kismayu last October to resolve the Galmudug crisis.
