All 96 passengers of the Philippine Air Force plane that crashed on Sunday killing 47 people have been accounted for, military chief Cirilito Sobejana said on Monday.
Forty nine military personnel were injured in the crash, Sobejana told Reuters.
The Department of National Defence said on Sunday three civilians on the ground were also killed, and four civilians were injured.
The Lockheed C-130 transport aircraft, carrying troops bound for counter-insurgency operations, overshot the runway after it touched down at Jolo airport in southern Sulu province, according to a military spokesman, Colonel Edgard Arevalo.
Defence Secretary Delfin Lorenzana said he had ordered an investigation of the incident, which would begin after rescue and recovery operations had been completed.
The military has not seen any sign of an attack on the plane.
Sulu, about 950 km (600 miles) south of the capital, Manila, is a stronghold of the militant Abu Sayyaf group, notorious for banditry and piracy, which the military has clashed with.