The talks seek to put an end to a conflict that goes back decades
Malaysian-led peace monitors have restarted operations in the southern Philippines province of Mindanao.
The monitors will oversee a ceasefire in areas where members of the Moro Islamic Liberation Front (Milf) and the Philippines army have been in conflict.
The Philippines government said their return meant the long-running peace talks were back on track.
The Milf has been fighting off and on for decades for autonomy from the Philippine government.
At least 100,000 people have been killed in the conflict and a further two million forced into refugee camps.
The two sides hope to reach a peace deal by April.
The head of the Philippines peace panel said the presence of the monitors would "strengthen the security, civilian protection and ceasefire monitoring in the conflict areas".
"With the deployment of the International Monitoring Team, peace talks are back on track," ambassador Rafael Seguis told reporters on Sunday.
Malaysia is brokering talks between the Philippines government and Milf rebels.
Officials told Reuters a one-day meeting would be held on Thursday to give both sides a chance to clarify their positions.
Mohaqher Iqbal, the rebels' chief negotiator, said his panel would attend the meeting to hear the government's proposals.
"We're not seeking to separate and create a new state," Mr Iqbal told Reuters.
"We're only asking the government to recognise our right for self-determination and we're not even trying to reclaim areas where Muslims have become a minority."
In February, the rebels rejected a power-sharing plan from the government, saying it would not give them enough autonomy.
The MNLF (Moro National Liberation Front) and the Milf have been fighting for greater autonomy in the south for four decades. Back in 1996, then-President Fidel Ramos reached a peace deal with the MNLF.
Talks to end the group's decades-long insurgency in the south of the country collapsed 18 months ago.
The Philippine Supreme Court blocked ratification of a deal after non-Muslims in the region objected that it posed a threat to their land ownership.
More than 1,000 people were killed and nearly 750,000 people were displaced by fighting between security forces and Muslim rebels from August 2008 until July 2009.
Analysts note that although it is often described in religious terms - pitting Muslims against a Catholic-dominant majority - the conflict has been focused on ownership of resource-rich land.
Muslims make up about 5% of the mainly Catholic Philippines and have long felt marginalised.
Analysts say the question now is whether the government will be able to implement any future deal before the end of current President Gloria Arroyo's term in June.