The first victim, reportedly a 55-year-old woman, died on April 21 in Iwate prefecture in northern Japan, an environment ministry official said.
Media reports said police were investigating two other deaths potentially caused by bears.
Of the two, one body was discovered elsewhere in the Iwate region on Thursday and another in a forest in Yamagata prefecture on Tuesday.
Police confirmed to AFP that two people had died but could not immediately verify other details.
Last year, Japan saw a spate of deadly bear attacks, with a record 13 people killed.
In the latest suspected attack in Iwate, Kumagai Chiyoko, 69, went missing after going to a mountain forest to pick edible wild plants, broadcaster NHK reported.
Police and rescuers launched a search on Thursday in the forest where her car was parked and found her body shortly after 8:00 am (2300 GMT Wednesday), NHK reported.
She reportedly had injuries on her face and head that appeared to have been caused by an animal’s claws.
City officials said local hunters were expected to begin patrolling the area on Friday, according to the broadcaster.
In the fiscal year between April 1, 2025 and March 31, 2026, bear attacks injured 216 people, according to environment ministry data.
This marked a sharp increase from the previous year, when three people died and 82 were hurt.
Scientists say the crisis is being driven by a fast-growing bear population, combined with a falling human population.
Last year also saw a poor acorn harvest pushing bears to seek food elsewhere.
Scrambling to respond, the government has deployed troops to help with trapping and hunting the animals.
Riot police have also been tasked with shooting them, with several thousand of the animals killed every year.
Brown bears are found only in the main northern island of Hokkaido, where their population has doubled over three decades to more than 11,500 as of 2023.
Japanese black bears, meanwhile, are common across large parts of the country including on the main island of Honshu which includes Iwate and Yamagata.
In 2024, the government added bears to the list of animals subject to population control, reversing protection that had helped the mammals thrive.