Hosi Koniyo, who was headed to an agriculture farm on the outskirts of northern Rangpur city in a rickshaw, was shot thrice in the chest, shoulder and hand by the yet-unidentified assassins.
"It appears to be a target killing as the assailants in masks shot him thrice. The Japanese gentleman died instantly," officer-in-charge of the local police station Rezaul Karim told PTI.
"Koniyo was alone in the rickshaw. They wore masks. As he reached the scene (they) shot him in the chest, shoulder and hand and then immediately fled the scene on a motorbike," said an eyewitness.
A frequent visitor to Bangladesh, Koniyo had been in Rangpur for the past six months and was familiar in the neighbourhood because of his philanthropic work.
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He had set up the farm, where he visited daily by a rickshaw, with help of a local businessman to grow grass for cattle.
The Islamic State militant group claimed the killing on Twitter, the SITE Intelligence Group -- a US monitoring organisation -- said.
The Japanese national's murder came five days after 50-year-old Italian aid worker Cesare Tavella was killed when motorbike-born terrorists shot him dead in Dhaka's diplomatic Gulshan area.
Islamic State group claimed responsibility for the fatal attack on Tavella. But Bangladesh government then downplayed the claim, describing it as an "isolated incident".
Security officials, either, have not ruled out that the IS could be using "local sympathisers" to carry out such attacks.