New Prime Minister Sanae Takaichi's government is scrambling to draft a special policy package to deal with the crisis, which has resulted in 12 deaths and more than 100 injuries since April.
Japan has strict gun laws and the troops will not carry firearms or hunt the animals.
They will instead arm themselves with bear sprays, sticks, shields, goggles, bullet-proof jackets and net launchers, the defence ministry said, as they attempt to restore a sense of safety in panicked communities.
A poor acorn harvest this year has triggered Japan's growing bear population to come into towns to seek food, particularly in northern regions such as Akita and Iwate, experts have said.
Rural depopulation has also blurred traditional boundaries between towns and bear habitats, encouraging bears to expand their habitats towards residential areas, according to researchers.
Japan's Self-Defense Forces agreed to offer logistical assistance to rural areas, including transporting bear traps, hunters and bears that have been caught.
A team of 15 soldiers was deployed on Wednesday to help move a trap in Kazuno city in the hard-hit Akita region.
Deputy Chief Cabinet Secretary Kei Saito said the military's focus was national defence, but they could help when possible.
Takaichi's cabinet held a special meeting on the crisis last week and said she would offer a policy package by mid-November.
That is likely to include increasing the number of hunters who can respond to the most urgent situations, such as bear sightings in residential areas.
Akita governor Kenta Suzuki, who has repeatedly warned that his region does not have the capacity to fight the animals, thanked the troops for their help.
"By coordinating efforts with local municipalities, I hope to assist the activities of the Self-Defense Force troops," Suzuki said at a signing ceremony in Akita with the military to mark the start of the programme
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