The C-130 Hercules transport plane was carrying 96 people, mostly fresh army graduates, when it overshot the runway on Sunday while trying to land on Jolo island in the southern Sulu province.

Witnesses and survivors told investigators the plane landed "hard" and then bounced twice before taking off again, said Lieutenant General Corleto Vinluan, chief of the Western Mindanao Command.

"Then at the right side of the airport it hit a tree -- that's the account of the injured," Vinluan told AFP.

Most of the dead were soldiers being deployed to the island -- a haven for Islamist militants -- as part of a counter-insurgency effort.

Three civilians who were not on the flight were also killed as the plane ploughed through coconut trees and houses.

Another 51 people, mostly troops, were injured. Many suffered severe burns when the four-engine aircraft exploded into flames.

The cockpit voice and flight data recorders, which are known as black boxes, will be sent to the United States for analysis, Vinluan said.

The CVR records flight crew conversations and the flight data recorder holds information about the speed, altitude and direction of the plane.

They could explain what caused the C-130, which the military said was in "very good condition", to crash in sunny weather.

"We will be able to hear from that black box what was the last conversation of the pilots and crew in the cockpit so we can ascertain the situation that really happened," armed forces chief General Cirilito Sobejana told CNN Philippines.

Photos of the scene released by the military showed the damaged tail and smoking wreckage scattered among trees.

Dental records are being used to help in the painstaking effort to identify badly charred bodies.

"So far we have identified six or seven of them," said Sobejana.

"We are doing our best... we need to bring them to their family at the soonest possible time."

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. Two others are being repaired while the third has been grounded following the crash.

Sunday's crash was one of the country's worst military air disasters and the latest in a series of 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 country's entire Black Hawk fleet.