Both the government and the Moro Islamic Liberation Front (MILF) peace panels said in a joint statement they were committed to completing the draft bill by August 18 so it could be passed by Congress as soon as possible.
"The panels have reached agreement on substantial portions of the document and have developed a shared understanding of the remaining challenges and unsettled issues, which they will bring back to their principals for further guidance," the joint statement said.
Asked what these challenges and unsettled issues were, head MILF negotiator Mohagher Iqbal said they included the draft law's "preamble," as well as "fiscal autonomy and inter-government relations".
"We covered many things but there were a lot of things that have not been resolved," he told AFP.
He said the government and MILF panels would have to meet again soon but would not say when this meeting would take place.
The joint statement said the two sides had discussed "fiscal autonomy and administration of justice," as well as the issue of budget transfers from the national government to the proposed Muslim autonomous government during the closed door talks in the southern city of Davao.
A peace pact signed in March committed President Benigno Aquino and the MILF to pass a law creating an autonomous Muslim region by 2016, when his six-year presidency ends.
In return, the 12,000-member MILF would disarm and help the national government to improve the lot of Filipino Muslims, who are among the poorest and most marginalised in the mainly Catholic nation of 100 million.
However drafting of the law has been delayed amid grumbling from some MILF quarters that the government was diluting the powers offered for the proposed autonomous area.
There are also growing fears that the autonomous region may not be created before Aquino's term ends. His political support has been crucial to the peace process.
Muslim rebels have been battling since the 1970s for independence or autonomy in the southern region of Mindanao which they claim as their ancestral home.
Tens of thousands of people have died in the conflict, while Mindanao has become one of the poorest and most corrupt regions in the Philippines.
Both the government and the MILF have also denied press reports that the talks were on the verge of collapsing.