The number of people killed in the Philippine Air Force plane crash on Sunday has reached 45, which includes civilians on the ground, the Department of National Defence said.

Five military personnel remain unaccounted for, the defence ministry said. The Lockheed C-130 transport aircraft carrying troops bound for counter-insurgency operations in the southern Philippines crashed with 96 aboard.

The aircraft crashed at Patikul in Sulu province, in the far south of the archipelago nation where the army has been fighting a long war against Islamist militants from the Abu Sayyaf and other factions.

Seventeen bodies had been recovered and 40 injured had been rescued so far, Defence Minister Delfin Lorenzana said in a statement.

Most of the 96 people aboard were troops flying from Laguindingan Airport, some 460 kilometres to the northeast.

“Rescue and recovery is ongoing,” Lorenzana said.

Pictures from the scene showed flames and smoke pouring from wreckage strewn among trees as men in combat uniform milled around. A large column of black smoke rose from the coconut palms into the blue sky.

Military chief Cirilito Sobejana said the plane had “missed the runway trying to regain power.”

A military spokesman, Colonel Edgard Arevalo, said there was no indication of any attack on the plane, but that a crash investigation had not begun and efforts were focused on rescue and treatment.

Sobejana said in a message to Reuters that the plane had crashed a few kilometres from Jolo airport at 11:30am (0330 GMT) and had been carrying troops.

“We are currently attending to the survivors who were immediately brought to the 11th Infantry Division station hospital in Busbus, Jolo, Sulu,” he said.

The island is about 950km south of the capital, Manila.

The Lockheed C-130H Hercules aircraft, registration 5125, had only arrived in the Philippines recently.

It was one of two aircraft granted by the United States government through the Defence Security Cooperation Agency, according to a government website announcement in January. It quoted an air force spokesman as saying the aircraft would provide enhanced capability for heavy airlift missions.

The website C-130.net said the plane that crashed had first flown in 1988. The model is a workhorse for armed forces around the world.

The Philippines armed forces have had a patchy air safety record. Last month a Black Hawk helicopter crashed during a training mission, killing six people.

A Philippines Air Force C-130 crash in 1993 killed 30 people.

A 2008 crash by the civilian variant of the Lockheed plane flown by the Philippines Air Force killed 11 people, according to the Aviation Safety Network.

In the country's worst plane crash, an Air Philippines Boeing 737 crashed in 2000, killing 131 people.