Lt. Colonel Luisito Angeles, commander of the Tactical Operations Group 5 of the Philippine Air Force (PAF), said the incident was caused by nose landing gear failure, causing the Fokker F27 to be stranded at the runway.
Angeles said the three pilots on board the plane, which came from Mactan Cebu, are all safe.
"They were here for a mission. We are doing our best effort to remove the aircraft in the runway as soon as possible," he said.
The PAF official said the plane is of 1990s model.
He said flights of Cebu Pacific planes were temporarily suspended.
A Philippine Air Force Fokker plane had a faulty landing around 9:45 a.m. May 11, 2015 at the Legazpi City Airport.