Cesar Simeon, 54, died at a hospital from blast injuries, said Esmeraldo Bensi, police desk officer at Mactan International Airport.
He said investigators were still trying to determine what caused the explosion. The Air Transportation Office (ATO) in Manila reported it was a grenade, but gave no other details.
Bensi said Simeon was alone inside his quarters on the ground floor beside the radar facility when the explosion occurred at about 2:15 p.m.
The area is near the runway but about two kilometers from the airports main terminal building.
Col. Arturo Evangelista, the investigating officer, said Simeon might have carried the grenade into the room or someone else might have thrown it through one of the windows.
He said he doubted the incident was an act of terrorism.
Bensi said the radar facility was not damaged and no flights were affected.
He said the windows in Simeons room were shattered and the concrete walls were pockmarked by shrapnel.
ATO chief Adelberto Yap said the radar facility serves the Visayas and parts of Mindanao.
The Mactan airport handles an average of 124 flights a day, 63 percent of which are commercial flights and the rest military or general aviation. Freeman News Service, Rudy Santos and wire reports