The draft of the proposed Bangsamoro Basic Law was to be reviewed by President Benigno Aquino before it is forwarded to Congress for approval, said presidential adviser on the peace panel Teresita Quintos Deles.
"Further discussions may be held based on the guidance of the president," she said.
The Moro Islamic Liberation Front submitted the document late Wednesday, just meeting the deadline that had been extended from Monday for the rebels to finish the draft in consultation with government representatives.
The MILF and the government in March signed a peace deal to establish the new Muslim autonomous entity called the Bangsamoro, or Muslim nation, by 2016 through a basic law to be passed by Congress and ratified in a plebiscite.
The Bangsamoro region would share political power with the central government and have substantial control over natural resources and revenues generated in the southern region of Mindanao, where 40 years of conflict has killed more than 100,000 and displaced millions.