Kunio Hoshi, 65, a Japanese citizen but born in Bangladesh, was attacked by unidentified assailants in Kownia in Rangpur district 335km (210 miles) north of the capital, Dhaka, and died on the way to hospital, police said.
The killing bore some similarities to the shooting death of an Italian working in Bangladesh, Cesare Tavella. Islamic State claimed responsibility for that attack, the first such claim the militant group has made in Bangladesh.
"This killing was also carried by three masked men who came by motorcycle and used a pistol, so the motives may be same," Bangladesh home minister Asaduzzaman Khan told Reuters.
