The fresh troops were geared up for battle in Sulu to beef up the battalions fighting Islamic rebel groups, but the transport plane crashed Sunday noon.
The ill-fated plane was recently procured from the US.
Latest reports said 45 people died after the Philippine Air Force C130H cargo plane crashed Sunday at Patikul, Sulu.
The plane was carrying more than 90 soldiers and crew.
Killed were 42 military personnel and three civilians.
Of the 53 injured, 49 were military personnel and four were civilians, the AFP said.
The civilians who died and injured were on the ground at the site of the crash.
About 50 persons were hospitalized after the crash, with some evacuated to Zamboanga City for further treatment, according to Joint Task Force Sulu.
Five soldiers on board the plane were personnel still missing, the task force said.
In a related report, 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.”
The Lockheed C-130 Hercules was one of two newly acquired transport aircraft that arrived in the country on January 29, procured by the PAF for P2.5 billion with funding aid from the US government.
The troops were supposed to beef up the battalions fighting against Abu Sayyaf, a Filipino jihadi group based in Sulu, accused of bomb attacks and piracy for decades.
The Abu Sayyaf proclaimed allegiance to ISIS in 2014.
The transport plane was bound for Jolo, Sulu’s capital, from Lumbia Airport (also known as Cagayan de Oro Airport), according to PAF.