Nearly 100 people, most of them recent army graduates, were on the C-130 Hercules transport plane which was trying to land on Jolo island in Sulu province around midday.
Some of the soldiers were seen jumping out of the plane before it hit the ground and exploded into flames, said Major General William Gonzales, commander of the Joint Task Force-Sulu.
According to armed forces, death toll jumps to 45 in Philippine military plane crash. It was one of the country's deadliest military aviation accidents. "This is a sad day but we have to remain hopeful," Gonzales said in a statement.
"We enjoin the nation to pray for those who are injured and those who have perished in this tragedy."
A search was still under way for 17 missing people.
Photos of the crash site released by the Joint Task Force-Sulu showed the damaged tail and the smoking wreckage of the fuselage's back section laying near coconut trees.
Images published by local media outlet Pondohan TV on its Facebook page showed the wreckage engulfed in flames and a plume of thick black smoke rising above houses located near the site.
Armed Forces Chief General Cirilito Sobejana said the aircraft was carrying troops from Cagayan de Oro on the southern island of Mindanao when it "missed the runway" as it tried to land on Jolo.
The plane tried to "regain power but didn't make it", he told local media.
The four-engine plane crashed near a quarry in a lightly populated area, First Lieutenant Jerrica Angela Manongdo said.
Western Mindanao Command chief Lieutenant General Corletan Vinluan told AFP the aircraft overshot the landing strip and broke into two according to initial reports.
Air force spokesman Lieutenant Colonel Maynard Mariano said the cause of the crash would be investigated, while armed forces spokesman Major General Edgard Arevalo told DZBB radio that it was being treated as an accident rather than an attack.
Most of the passengers had recently graduated from basic military training and were being deployed to the restive island as part of a joint task force fighting terrorism in the Muslim-majority region.
They were supposed to report for duty on Sunday, Gonzales said.
The military has a heavy presence in the southern Philippines where militant groups, including the kidnap-for-ransom outfit Abu Sayyaf, operate.
DEADLY ACCIDENTS
C-130s have been the workhorses of air forces around the world for decades, used to transport troops, supplies and vehicles. They are also often deployed to deliver humanitarian assistance and disaster relief.
The Hercules that crashed Sunday has the same tail number as one acquired from the United States and delivered to the Philippines earlier this year.
Senator Richard Gordon said it was the fourth military aircraft accident this year with "mass casualties".
"Are we buying defective crafts... (with) the people's money?" he tweeted.
Presidential spokesman Harry Roque described the accident as "very unfortunate", and the US embassy Charge d'Affaires John Law offered "sincerest condolences" to the families of the victims.
Sunday's accident comes after a Black Hawk helicopter crashed last month during a night-time training flight, killing all six on board. The accident prompted the grounding of the Philippines' entire Black Hawk fleet.
