Rebels have expressed frustration at the slow pace of the peace process
Muslim rebels are beginning to withdraw from villages in the southern Philippines after the government threatened to take action against them.
Some 800 rebels from the Moro Islamic Liberation Front (MILF) have occupied villages in North Cotabato province, displacing about 6,500 people.
However one report suggests some rebels have been resisting orders to leave.
There has been controversy in the region over a deal to expand a Muslim autonomous zone there.
The government and MILF rebels had been set to sign a preliminary accord on Tuesday on the deal, which would see the zone expanded in exchange for the end of a decades-long insurgency.
But on Monday the Supreme Court suspended the deal, following complaints from Christian lawmakers in the region.
On Thursday, Interior Minister Ronaldo Puno warned rebels they had 24 hours to leave or face forcible eviction.
Government and security officials confirmed on Friday that some rebels were withdrawing from the occupied farms and villages in the predominantly Christian province of North Cotabato.
But some were refusing to follow orders from the leadership, said military spokesman Lt Col Ernesto Torres.
"We are presently dealing with a recalcitrant group of MILF which appeared to be disregarding the call of their leaders to vacate certain areas in North Cotabato," he said, according to Reuters news agency.
"We will apply proportionate and justifiable force, whenever necessary, to ensure that laws are upheld and peace is restored in the province."
But the rebel vice-chairman Ghazali Jaafar was quoted by Associated Press as saying the withdrawal would be gradual, "because these people are armed and the civilians might panic if there is a sudden repositioning".
Reports say many of the occupied villages are on the provincial border of mainly Christian North Cotabato and mainly Muslim Maguindanao, which contains some large rural MILF camps.
The rebels are said to be frustrated at the fresh obstacles towards agreeing to expand the Autonomous Region of Muslim Mindanao (ARMM).
Regional tensions have grown since the plan was agreed, with Christians fearful of the greater powers that would be granted to rebels.
The expanded zone, which would be subject to approval in a local plebiscite, would include another 712 villages.
Local leaders would also be entitled to a large share of the region's rich resources.