It has also advised its nationals to limit movement.
Hoshi was gunned down in Rangpur on Saturday, five days after Italian aid worker Cesare Tavella was killed in a similar way at Dhaka’s diplomatic zone Gulshan.
The Japan embassy in Dhaka did not issue any official statement after the killing, but it was in close touch with the government to get details of the murder.
The embassy spokesperson Takeshi Matsunaga told bdnews24.com by telephone on Sunday the embassy staff had a meeting after the incident.
“We have informed Japanese nationals about the murder and advised them to immediately maintain greater vigilance,” he said.
He said after the Islamic State’s claim of the murder they issued another statement to their nationals in Japanese language in their Facebook page.
“We encouraged them to maintain vigilance to avoid potential risk, and not to travel unnecessary,” Matsunaga said.
“We condemn this despicable act in the strongest possible term and urge the government to conduct investigation and bring the perpetrators to justice.”
Police have detained six suspects in connection with the shooting at Kaunia Upazila's Alutari village in Rangpur.
The killing bore some similarities to the gunning down on Sep 28 of Italian Tavella.
One of the detainees was a rickshaw puller who was taking Hoshi to his farm in that village and another was the owner of a residence near where the attack took place.
Islamic State had also claimed responsibility for killing Tavella, its first such claim in the country.
Prime Minister Sheikh Hasina, however, said there was no presence of IS in Bangladesh.
Attacks on foreigners are rare in Bangladesh. But these two incidents in a week shook the diplomatic community amid the global security concerns.
EU Ambassador in Dhaka Pierre Mayaudon at a discussion on Saturday on the International Day of Non-violence said “should investigations conclude that Cesare and Kunio were killed because they were foreigners, this would open an unprecedented and sombre chapter of violence in this country”.
Citing the recent incidents across the world, he had said international environment “is indeed a source of much concern”.
“Violence comes in all sizes and shapes. No country, industrialised or developing, is safe,” he said.
“No segment of any society can consider itself immune to violence or human rights violation. It has obviously a lot to do with terrorism, but not just that,” Ambassador Mayaudon added.