The shooting took place Saturday when a 22-year-old sergeant, surnamed Lim, opened fire on members of his own unit at a guard post near the tense border with North Korea, killing five and wounding seven.
Lim was captured alive Monday after a 24-hour standoff with thousands of troops ended when he shot himself in the chest.
Minister Kim Kwan-Jin had infuriated the families of Lim's victims when he suggested, in a recent meeting with lawmakers, that bullying had been a factor behind the shooting spree.
"We will thoroughly bring the truth to light in order not to damage the reputation of the victims," he said.
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Barrack-room bullying is a sensitive issue in South Korea, where the vast majority of personnel are those serving their mandatory two-year military service.
Mistreatment of fresh conscripts used to be rampant and was blamed for a number of suicides and similar shooting sprees in the past.
Measures have been taken to stamp out the practice, but experts say those who struggle to adapt to military life are often isolated and humiliated.
He had difficulty adapting to the military, and psychological evaluations had advised senior officials to pay special attention to him.
Before his unsuccessful suicide attempt, Lim wrote a suicide note that media reports say detailed how bullying drove him to despair.
The defence ministry has refused to release the note or confirm its contents.