People in Mindanao want a peace deal, but so far it is proving hard to achieve
Both fighters and civilians in the Philippines have expressed concern about the withdrawal of international peace monitors from the restive south.
Peace talks collapsed, and fighting resumed, after the Supreme Court blocked a peace deal in August.
The Philippine government has just begun appointing a new panel for peace talks with Moro rebels.
But this was too late to prevent the departure of the last 12 Malaysian peace monitors over the weekend.
The Malaysian peacekeepers had led an international monitoring team in the region, aimed at safeguarding a ceasefire dating from 2003.
A statement from the Moro Islamic Liberation Front (MILF) said it regretted the withdrawal, but stressed that Malaysia must not be blamed.
Rather it was the failure of the Philippine government and the MILF to reach agreement on how peace talks should proceed, said Mohagher Iqbal, chairman of the MILF negotiating panel, as quoted on the MILF website.
A long-time observer of the Mindanao conflict, Alan Davis of the Institute for War and Peace Reporting, said the Malaysian withdrawal was unfortunate as they had been the "honest brokers" on the ground.
Fighting has resurged in Basilan in recent days, and a military commander there told local reporters that the situation was still tense.
For the monitors to stay in Mindanao, an extension of their mandate was required under the auspices of new peace talks.
The government said on Monday it was beginning to appoint a new peace negotiating panel, after the dissolution of the previous panel in September.
The new panel will be led by foreign undersecretary Rafael Seguis, and its composition will be complete by mid-December, the government said.
But it remains unclear when renewed peace discussions will begin.
Foreign governments, including the British, US and EU, have said in recent weeks that they hope a return to talks can be managed soon.
A Memorandum on Ancestral Domain, a first step toward a comprehensive peace deal, was due for signing in August but was rejected by the Supreme Court after protests by Christian communities in areas likely to be affected.
Violence erupted again, displacing at least half a million people in the area, and leaving several hundred people dead.
The government says its new approach to a peace deal is focused on disarmament, demobilisation and reintegration.
MILF leaders say they cannot return to talks unless the memorandum is honoured.