Jesus Dureza, who is leading a four-member government peace panel, said the meeting with three representatives from the Moro Islamic Liberation Front (MILF) to resume negotiations went well despite recent unrest.
"There is earnest effort on both sides to have peace in Mindanao," he told reporters, but said further details would be issued in a joint statement the following day.
The MILF panel, led by lawyer Lanang Ali, could not be reached for comment.
Earlier, Dureza said the fact that other armed groups and "terror elements" were operating in areas dominated by the MILF in Mindanao complicated the negotiations.
He said it would be a long road toward a peace pact as they would have to address other issues such as tackling the root cause of the rebellion, improving the livelihood of the people and social inequities.
Malaysia has long hosted formal negotiations between Manila and the 12,500-strong MILF, which has been waging a 25-year insurgency to establish an independent Islamic state in the southern Philippines.
MILF spokesman Eid Kabalu told AFP on Wednesday that the rebels expected the government to present its proposal to resume formal peace talks but warned against hopes for an early peace.– AFP