Teresita Deles, President Gloria Arroyo's adviser on the peace process, said both sides had reached agreement on fresh negotiations late on Tuesday in Kuala Lumpur.
Malaysia, negotiating efforts to halt a three-decade conflict that has killed 120,000 people, hosted an informal meeting this week of negotiators from the Philippine government and the Moro Islamic Liberation Front (MILF).
The 11,000-strong MILF is the largest of several Muslim separatist groups in this mainly Roman Catholic nation.
"We are confident that the resumption of talks is a big step towards the forging of peace with the MILF soon," Deles said.
She said the government peace panel, led by Arroyo's communications director Silvestre Afable Jr and retired general Rodolfo Garcia, was returning from Malaysia on Wednesday and would brief the president on the informal meeting.
Both sides are expected to meet in Kuala Lumpur next month to discuss the agenda for the formal talks.
A ceasefire between troops and MILF separatists has held since July 2003, partly helped by the presence of 60 peace monitors from Malaysia, Brunei and Libya.