A bear that attacked a supermarket employee in northern Japan at the weekend before apparently holing up inside for three days has been exterminated after being found in a trap local authorities had laid near the store’s entrance.

A 47-year-old man was taken to hospital suffering from facial and other injuries after the attack in the northern prefecture of Akita on Saturday morning. His injuries are not life threatening, according to local media.

Police called in licensed hunters to kill the animal, which is said to be about a metre in length, but they were initially unable to locate it, the Kyodo news agency said.

Traps were laid at entrances to the supermarket, where the bear appeared to have eaten large quantities of meat. A drone had also been deployed to establish its whereabouts.

Police said the bear had been found in a trap, where honey, apples and bread had been placed, set between an entrance and a storage area after the government informed them the trap’s sensor had been activated early on Monday morning.

The bear was put to sleep before being killed, the Kyodo news agency said.

Authorities in parts of northern Japan are struggling to address the rising number of encounters between humans and bears that have left their natural habitat in search of food.

Residents have been told to remain vigilant, including those in urban areas, as the animals prepare to go into hibernation, while some have warned that the scarcity of food means that some hungry animals will continue to forage during the colder months.

Authorities reported 219 casualties, including six deaths, from bear attacks across 19 of Japan’s 47 prefectures in the 12 months to March this year – the highest figure since nationwide data became available.

Fluctuating harvests of bears’ staple foods and rural depopulation have been cited as factors in the rise in ursine encounters, while experts believe a steady fall in the number of children, whose noisier behaviour helps keeps bears away, is another factor behind the rise in incidents in country towns and villages.

The injured man in Akita was attacked while working near the supermarket’s delicatessen section before the store opened early on Saturday. Another worker helped him to the safety of a storage area before calling police, Kyodo said. The store was closed and there were no shoppers inside at the time.

Several bear sightings had been reported in the neighbourhood, located near the centre of Akita city, in recent days. The prefecture was the scene of two high-profile incidents last year, including one in which a man lost part of an ear after finding a bear in his garage, and another in which several people were mauled at a bus stop.

Japan’s bear population is growing, with one estimate putting the number of black bears at 44,000 – compared with 15,000 estimated in 2012. That figure does not include Hokkaido, thought to be home to just under 12,000 Ussuri brown bears, whose population has more than doubled since 1990.