The Rapid Action Battalion (RAB) arrested them from Chapai Nawabganj, an area 210 kilometres from Rangpur where 66-year-old Hoshi Kunio was gunned down on October 3.
His murder came less than a week after Italian aid worker Cesare Tavella was shot dead in similar fashion in Dhaka. That attack also was claimed by the Islamic State.
"We (RAB) arrested the trio last night based on a secret tip off...They (detained suspects) have confessed their involvement in Kunio Hoshi's murder," RAB's unit commander in northwestern Chapai Nawabganj Lieutenant Colonel Mahbub Alam told PTI.
"When we pressed them, they admitted their guilt saying they were hiding in Chapainawabganj" after murdering Hoshi in Rangpur on October 3, Alam said.
Asked if they had any local or foreign Islamist links or their political connections, he said "we could not find it out and we did not find much time to quiz them either".
"We have already handed them over to police and may know the details once they were interrogated by the concerned investigation officials," Alam said.
Two small firearms, bullets and machetes were seized from them, Alam told reporters.
All three have pending criminal cases, including those of murder and mugging, he said.
Their families, however, claim they had been picked up by 'plain clothesmen' last month, but both Rangpur police and RAB have denied these allegations.
The Islamic State had claimed the responsibility for the attack. The government had rubbished the claim.
Prime Minister Sheikh Hasina had said earlier this month a series of clandestine attacks and assassinations were carried out in a planned way in recent months and they were attributed to international Islamist outfits to "portray Bangladesh as an unsafe country to expose it to foreign (military) attacks like in Pakistan".
