The militants were held in a crackdown as raids were conducted in different parts of the capital, Maksudul Alam, assistant director of Rapid Action Battalion (RAB) legal and media wing said.
Among the 12 arrested are -- Mufti Mainul Islam, Bangladesh's chief coordinator of Al-Qaeda in the Indian Subcontinent (AQIS), and his advisor Maolana Zafor Amin, he said.
"Huge stash of explosives, bomb-making materials, knives, training and jihadi books were seized from their possession," Alam said.
AQIS had been planning an attack in the Muslim-majority nation after Eid-ul Fitr, Commander Mufti Mahmud Khan, the most senior RAB spokesman, told reporters.
"They've selected a madarsa in (the northern district of) Bogra for training," he said.
The group was financed by individuals from Saudi Arabia and United Arab Emirates, he added.
AQIS has claimed responsibility for the murder of secular bloggers Avijit Roy and Ananta Bijoy Das, who were brutally murdered this year.
Bangladesh recently banned Ansarullah Bangla Team (ABT), suspecting its involvement in bloggers' murders and having links to al-Qaeda.
Police's intensified clampdown came as last month ABT sent out letters in AQIS' name, threatening to kill 10 prominent Bangladeshis, including Prime Minister Sheikh Hasina's adviser H T Imam, vice chancellor of premier Dhaka University Professor Arefin Siddique and popular writer and physicist Professor Zafar Iqbal.
AQIS is an al-Qaeda affiliate for militant activities in South Asia.
In September last year, al-Qaeda launched a new branch to "wage jihad" in South Asia to invigorate its waning Islamist extremist movement.
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