The C-130 Hercules transport plane was carrying 96 people, most of them recent army graduates, when it overshot the runway while trying to land on Jolo island in Sulu province.
Philippine security forces are searching among coconut trees on a remote southern island for the flight data boxes of an aircraft that crashed and killed 52 people in one of the country's worst military air disasters.
The plane "skidded" and burst into flames in a village, killing 52 people including 49 military personnel and three civilians, said military spokesman Major General Edgard Arevalo.
Another 51 were injured, most of them soldiers. It was not clear if the pilots were among the survivors.
Colonel Arevalo said the Lockheed C-130 transport aircraft that crashed at the weekend, was in "very good condition", followed specified operating protocols and had 11,000 flying hours remaining before its next maintenance.
The Hercules C-130 transport plane was carrying 96 people, most of them recent army graduates, when it overshot the runway while trying to land in sunny weather on Jolo island in Sulu province – a haven for militants – on Sunday.
The three people killed on the ground had been working in a quarry, village leader Tanda Hailid said.
Photos of the scene released by the Joint Task Force-Sulu showed the damaged tail and the smoking wreckage of the fuselage's back section laying in a coconut grove.
"We have people on the ground to make sure the integrity of the pieces of the evidence that we will retrieve, most particularly the flight data recorder," Arevalo said.
"Aside from eyewitness accounts, we are also looking for recordings, radio conversation recordings between the pilot and the control tower."
Arevalo said the military had secured the crash site and would ensure that militants on the island did not disrupt search efforts.
Most of the passengers had recently graduated from basic military training and were being deployed to the restive island as part of a counter-insurgency effort in the Muslim-majority region.
The military has a heavy presence in the southern Philippines where militant groups, including the kidnap-for-ransom outfit Abu Sayyaf, operate.
"This is one of the worst tragic incidents that happened in our armed forces," said Arevalo.
C-130s have been the workhorses of air forces around the world for decades, used to transport troops, supplies and vehicles.
The second-hand Hercules that crashed Sunday was acquired from the United States and delivered to the Philippines earlier this year.
It is one of four in the country's fleet. Two are being repaired while the other one has been grounded following the crash.
"These are all seasoned and experienced pilots that's why we are also unable to immediately say how this came into being," said Arevalo.
"Even if these (military assets) are not brand new... these are airworthy or seaworthy or landworthy."
The accident was the deadliest for the Philippine air force, said Jose Antonio Custodio, a military historian and analyst.
This ranks as the worst crash of a Philippine military aircraft with 50 dead so far as compared to the 40 dead in a 1971 crash of a PAF C-47," Custodio told AFP.
It was the latest in a series of air force accidents this year.
Last month, a Black Hawk helicopter went down during a night-time training flight, killing all six on board. The accident prompted the grounding of the Philippines' entire Black Hawk fleet.