The Rapid Action Battalion (RAB) also seized explosives and other bomb-making materials during raids on Wednesday on the militants' hideouts in the capital Dhaka, spokesman Major Maksudul Alam said.
"During the raids we arrested 12 militants including Maolana Mainul Islam who is the chief coordinator of AQIS in Bangladesh," RAB's Alam told AFP.
Read: Al Qaeda suspects among 1,200 militants to escape in Yemen prison break
Al Qaeda in the Indian Subcontinent (AQIS) had been planning an unspecified attack in the Muslim-majority nation after Eidul Fitr, which celebrates the end of Ramazan, Commander Mufti Mahmud Khan, the most senior RAB spokesperson, told reporters.
"They've selected a madrassa in (the northern district of) Bogra for training," he said, adding that the group was financed by individuals from Saudi Arabia and United Arab Emirates.
AQIS has claimed responsibility for the murder of several secular bloggers in Bangladesh this year, including the hacking to death of Bangladeshi-born US citizen Avijit Roy in Dhaka in February.
Read: Press briefing: ‘Those killed in Sunday raid were al Qaeda operatives’
Last September, al Qaeda released a video announcing the establishment of a branch on the Indian subcontinent, AQIS, saying it wanted to revive militant activity.
Bangladesh, home to the world's fourth largest Muslim population, has not been hit by a major militant attack since 2006.
Although the country has in recent years witnessed a rise in support for a hardline political group, experts say there is little appetite for religious extremism in the country. There are also no known cases of Bangladeshis joining the Islamic State group.
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