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The C-130 military plane was transporting troops from Cagayan de Oro, in Mindanao, to Sulu province when it missed the runway on the island of Jolo, CNN affiliate CNN Philippines reported, citing Armed Forces Chief Cirilito Sobejana.
The plane, which was carrying 96 military personnel and crew, crashed into nearby Patikul village at 11:30 a.m. local time on Sunday (11:30 p.m. ET).
"Minutes after the crash, troops and civilian volunteers rushed to the site for search and rescue. Per eyewitnesses, a number of soldiers were seen jumping out of the aircraft before it hit the ground sparing them from from the explosion caused by the crash," according to a press release by Joint Task Force Sulu.
All victims have now been accounted for. Maj. Gen. Edgard Arevalo, a spokesman for the military, said 47 army personnel died, while 49 survived the crash and are being treated in hospitals. Three civilians on the ground were killed and four were injured, Arevalo said.
He added that the soldiers on the flight were fresh graduates and had just completed military training.
An investigative team arrived Monday to look for the plane's flight data recorder and probe what caused the crash. They will also look into the reports of soldiers jumping from the plane.
Images from a local TV station appeared to show the burning wreck of the plane and thick smoke billowing from the village. A large plume of smoke is seen in images of the crash rising up through the palms to the blue sky.
Joint Task Force Sulu Commander William N Gonzales said the personnel traveling on the plane "were supposed to report to their battalions today. They were supposed to join us in our fight against terrorism."
This is the country's worst military air disaster in around 30 years, Reuters reported. In 1993, a Philippine Air Force C-130 crashed, killing 30 people.
The plane was considered to be in good condition. It had 11,000 flying hours left before it was due for maintenance.
All C-130s in the Philippines will now be grounded as part of the military's standard operating procedure. However, the military only has one other C-130 in the country -- the other two in the fleet are overseas for maintenance.