He is accused of killing 42 people, arson and loot at ‘Shankharikathi Bazar’ in Bagerhat’s Kachua Upazila during Bangladesh’s 1971 Liberation War.
The killings came to be known as ‘Shankharikathi massacre’.
Khan’s arrest comes nearly 10 days after the International Crimes Tribunal, set up to try war crimes during the Liberation War, issued a warrant against him on June 10.
The 60-year-old was picked up from the house of a businessman in the Rajshahi metropolitan area in the early hours of Friday, said detective police OC Nur Hossain Khandker.
He hails from Bagerhat’s Morelganj Upazila.
On June 11, police arrested another accused in the case, Abdul Latif Talukdar.
OC Hossain said Khan had been kept at the city’s Rajparha police station and would be sent to Dhaka in the afternoon.