In a joint-statement posted on a government website, the sides signaled their readiness to ensure security in the Mindanao region.
The parties "resolved to strengthen their cooperation and coordination in addressing security concerns in the most effective and appropriate manner, and also in rebuilding trust and public confidence in the peace process," the statement said.
The decommissioning process, set to be managed by an independent body with a Turkish expert at the helm, will consist of four phases.
During the first phase, the MILF should make an inventory of its militants' weapons, as it is supposed to get financial assistance.
In the second and third phases, the independent body will receive 30 percent and 35 percent of the weapons, respectively, with the rest due to be decommissioned during the last phase.
"The parties shall undertake measures to promote and guarantee free movement and create an environment free of fear and intimidation," the protocol said.
Philippine President Benigno Aquino has repeatedly called for a peace agreement between the government and the rebels, who he said should put an end to the MILF's 40-year insurgency, one which has already killed about 200,000 people.
The deal, signed in 2014, obliges the MILF to stop its pursuit of a separate Islamic state in the southern Philippines in exchange for more power and money.