The 23 leaders attending the negotiations in Nairobi on Sunday agreed the federal system would include district, regional and state administrations to reflect the level of local administrations already in place.
Kenyan diplomat Bethuel Kiplagat, the talks’ chief mediator, said agreement on the transitional charter was a “very, very important stage”.
Kiplagat added 360 Somali delegates will discuss the charter on Monday.
If the proposals are adopted, the talks will move into their final stage which will focus on power sharing.
This will include the election of a president and the appointment of 351 members of parliament, based on Somalia’s complex clan system.
Talks broke up three weeks ago when representatives disagreed over the type of federal system for the country.
At least two northern regions, Puntland and Somaliland, have had their own administrations for several years.
Somaliland has even been seeking international recognition as a separate country and has not taken part in talks.
A further concern is that many important and influential figures have failed to turn up.
Among those absent from the talks was Abd al-Qasim Hasan, president of Somalia's Transitional National Government.
Some of the countries underwriting the cost of the talks also felt "the conference will not be broad-based enough without the presence of these people”, James Kiboi of the Inter-Governmental Authority on Development.
History of failure
The latest series of talks to end the chaos in the country began last October, the twelfth such talks.
To date, the transitional government elected at a peace conference in neighbouring Djibouti in August 2000 has had little influence outside the capital Mogadishu and has not been able to disarm armed factions.
There has been no effective central Somali government since the 1991 ouster of dictator Muhammad Siad Barre.