The C-130 Hercules transport plane was carrying 96 people, most of them recent army graduates, when it overshot the runway on Sunday while trying to land on Jolo island in Sulu province -- a haven for Islamist militants.

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.

"This is one of the worst tragic incidents that happened in our armed forces," Arevalo said.

The three civilians killed were not on the flight and had been working in a quarry, village leader Tanda Hailid told AFP.

They were relatives of Agga Ahaddi, who was lucky to survive the crash. He and his child were outside when the plane ploughed through their house and then a neighbour's home.

"We ran away, we just left," Ahaddi told AFP.

Photos of the scene released by the military's Joint Task Force-Sulu showed the damaged tail and smoking wreckage scattered 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 militants on the island do not disrupt search efforts.

Dental records were being used to help identify the charred remains of victims.

Most of the passengers 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.

- 'Worst crash' -

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 was one of four in the country's fleet and was in "very good condition", the military said. Two others are being repaired while the third 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... (happened)," said Arevalo.

"Even if these (military assets) are not brand new... these are airworthy."

"This ranks as the worst crash of a Philippine military aircraft," Jose Antonio Custodio, a military historian and analyst, told AFP.

It was the latest in a series of recent military air accidents in the Philippines.

Last month, a Black Hawk helicopter went down during a night-time training flight, killing all six onboard. The accident prompted the grounding of the country's entire Black Hawk fleet.

President Rodrigo Duterte's spokesman Harry Roque said Monday the incidents would provide "impetus for further modernisation" of the armed forces.

"The whole country is mourning," he said.