The operation began in Kazuno, a small town nestled among forested mountains that has registered a sharp rise in bear sightings.
For weeks, residents have been urged to avoid the thick woods and stay indoors after dark to keep clear of bears foraging near homes for food.
"Even if just temporary, the SDF's help is a big relief," said Yasuhiro Kitakata, who oversees the town's bear department.
"I used to think bears would always run away when they heard noise but now they actually come toward you. They're truly frightening animals," he added.
There have been more than 100 bear attacks with a record 12 people killed across Japan since April, according to the environment ministry.
Two-thirds of those deaths were in Akita prefecture, where Kazuno is located, and nearby Iwate.
In Akita, authorities say bear sightings have jumped six-fold this year to more than 8000, and attacks are on track to set a new record, prompting its governor to request help from the Self-Defence Forces last week.
"The townspeople feel the danger every day," Kazuno mayor Shinji Sasamoto said after meeting about 15 soldiers who rolled into town in an army truck and jeeps, equipped with body armour and a large map.
"It has affected how people live their lives, forcing them to stop going out or cancel events," Sasamoto said.
The troops were there to transport, set and inspect the steel-barred traps used to capture bears that are later shot by trained hunters hired to cull the population.
Defence Minister Shinjiro Koizumi said on Tuesday the bear mission aims to help secure people's daily lives but that service members' primary mission is national defence and they cannot provide unlimited support for the bear response.
The Japanese Self-Defence Forces are already understaffed.
So far, the ministry has not received requests from other prefectures for troop assistance over the bear issue, he said.
On a mountain road outside the town, local forestry officials showed soldiers how to assemble and load the traps onto trucks.
The white-helmeted troops carried bear spray and were guarded by others with shields and long wooden poles shaped like rifles usually used for bayonet drills.
After Kazuno - a town of about 30,000 people known for its hot springs, scenery and variety of sweet apples - the soldiers will head for the cities of Odate and Kitaakita under an agreement lasting until the end of November.
In recent weeks, bears have attacked customers inside a supermarket, jumped a tourist waiting at a bus stop near a UNESCO World Heritage site and mutilated a worker at a hot spring resort.
Some schools have temporarily closed after bears were spotted wandering around their grounds.
Bear attacks usually peak in October and November as the animals forage intensively before winter hibernation.
Japanese black bears, common across most of the country, can weigh up to 130kg.
Brown bears on the northern island of Hokkaido can weigh as much as 400kg.
It is not the first time Japan has deployed troops to assist in wildlife control.
The military provided aerial surveillance for hunts of wild deer around a decade ago and culled sea lions to protect fisheries in the 1960s.
Japanese authorities will this month announce a package of emergency measures to deal with the bear problem including recruiting more licensed hunters, Deputy Chief Cabinet Secretary Kei Sato told a press conference.
In September, the government relaxed gun rules to make it easier for hunters to shoot bears in urban areas.
with AP
