Unspecified military units guarding the Buliok complex completed a three-day redeployment on Thursday in keeping with an agreement with the Moro Islamic Liberation Front (MILF) in February, a military statement said.
Malaysia has pledged to host the resumption of negotiations expected later this year as President Gloria Arroyo bids to bring a political settlement to three decades of rebellion by the Roman Catholic nation's large Muslim minority.
"The pullout is seen as a gesture of faith and good will on the government's part as the peace talks resume between the state and the MILF," the statement said.
Arroyo ordered the military to seize Buliok, near the town of Pikit, last year on grounds MILF units in the area sheltered terrorists and kidnappers.
The MILF signed a ceasefire with Manila 14 months ago after the fighting left more than 150 people dead.
The military's Southern Command said the units from Buliok redeployed to the Lanao region of Mindanao island.
It did not say how many soldiers had been pulled out from Buliok, but the military had said in the past that more than 2,000 soldiers, mostly marines, were stationed in the area.