The Moro Islamic Liberation Front (MILF) signed the peace agreement in March, but it fell into serious question amid a row over a draft law to create a Muslim self-rule area in the south of the mainly Catholic nation.
"After a series of productive meetings... We have concluded discussions on the various issues involving the draft Basic Bangsamoro Law," President Benigno Aquino's chief aide Paquito Ochoa and chief MILF negotiator Mohagher Iqbal said in a joint statement.
The Aquino government and the MILF signed an accord in March that laid out a roadmap for final peace by the middle of 2016.
The deal called for MILF control of a new southern autonomous region, and the rebels would lay down their arms.
More From This Section
However, the process ran into difficulties after a draft bill creating the autonomous region was submitted to Aquino for review in April by a joint commission of MILF and government representatives that drew up the document.
The joint statement said the resolutions arrived at by both parties since the new talks began on August 1 "will be incorporated into the final draft Basic Bangsamoro Law that will be prepared and submitted to" Aquino.
The statement did not discuss the details of these resolutions.
The fresh talks were seen as crucial to keep the peace roadmap on schedule, allowing time for Congress to pass the self-rule law by the end of this year or early next year.