Ahmed Mohamed Islam Madobe of Jubaland and Said Abdullahi Deni have been in the Somali capital Mogadishu since Wednesday ahead of the talks.
Both Nadobe and Deni have voiced opposition to a deal reached in August for elections to be held using a so-called constituency caucuses, a departure from a controversial polling system in which clan heads vote to determine the country's leader.
They have not been part of a meeting of Somali regional leaders in the town of Dusamareb where the deal was struck.
Galmudug, Hirshabelle, South West and Banadir leaders have been part of the meeting which emerged with a 17-point resolution which among other things resolved that elections will be held in Somalia every four years using the constituency caucus.
Somalia's National Independent Electoral Commission (NIEC) has been endorsed as the sole organiser of future elections in the regions forming part of the federation.
Under the new system, the federal president will be elected by 275 MPs after their own election by 301 delegates.
Somalia has been with a weak federal government since the overthrow almost thirty years ago of former strongman Siad Barrie.