Philippine authorities ordered an investigation on Monday into the crash of an Air Force plane that overshot a runway and killed more than 50 people, including civilians, in the country's worst military air accident in nearly three decades.

With all 96 passengers accounted for, the death toll from the crash rose to 52, including three civilians, after two of 49 injured soldiers succumbed to their injuries on Monday, the defence ministry said.

Military spokesman Edgard Arevalo said the plane was in "very good condition" and had 11,000 flying hours remaining before its next maintenance was due.