Nine other people were also wounded in the rampage at an army camp on the southern island of Basilan, a hotbed for Muslim extremist groups, said Colonel Benjamin Hao.
"There was a bible study (session). He went there, to back (of the room) and then suddenly opened fire," Hao told reporters.
Responding soldiers shot the gunman dead but the motive for the attack remained unknown.
"His battalion commander said that he had changed after going on vacation. He was surprisingly quiet. Before that, he was talkative, kind of jolly, but when he came back, he was different," Hao said.
"We believe it is an isolated incident but we will look closer into its medical and psychological aspect in order to determine the root cause," he said.
Soldiers in the island of Basilan face numerous threats, battling Muslim armed groups like the Al-Qaeda-linked Abu Sayyaf, which has been blamed for the Philippines' deadliest terror attacks.
The group, which hides in the thickly-forested hills of Basilan, has been behind beheadings and kidnappings of foreign tourists and Christian missionaries as well as bomb attacks.
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