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 bottom and exploded into flames, said Major General William Gonzales, commander of the Joint Task Force-Sulu.
It was one among the country's deadliest military aviation accidents.
"This may be a sad day but we've to stay hopeful", Gonzales said during a statement.
"We enjoin the state to wish for those that are injured and people who have perished during 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 therefore 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 location .
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" because 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 during a lightly urban area , lieutenant Jerrica Angela Manongdo said.
Western Mindanao Command chief lieutenant general Corletan Vinluan told AFP the aircraft overshot the airstrip and broke into two consistent with initial reports.
Air force spokesman lieutenant colonel Maynard Mariano said the explanation for the crash would be investigated, while soldiers spokesman Major General Edgard Arevalo told DZBB radio that it had been being treated as an accident instead of an attack.
Most of the passengers had recently graduated from basic training and were being deployed to the restive island as a part of a joint task force fighting terrorism within the Muslim-majority region.
They were alleged to report for duty on Sunday, Gonzales said.
The military features a heavy presence within the southern Philippines where militant groups, including the kidnap-for-ransom outfit Abu Sayyaf , operate.
C-130s are the workhorses of air forces round the world for many years , wont to transport troops, supplies and vehicles. they're also often deployed to deliver humanitarian assistance and disaster relief.
The Hercules that crashed Sunday has an equivalent tail number together acquired from the us and delivered to the Philippines earlier this year.
Senator Richard Gordon said it had been 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 therefore the US embassy Charged 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.
