The 60-year-old extremist, identified as Garibullah Akand, was arrested in Muktagachha of northern Mymensingh area along with 26 suspected militants, police said.
Akand was a close associate of Jamaatul Mujahedeen Bangladesh's executed leader Siddikul Islam Bangla Bhai, Muktagachha police station's chief Fazlul Karim said.
Akandh was being looked for a number of murder and terrorist charges as an associate of Bangla Bhai, who was executed in 2007 after trial along with three other top leaders of the militant outfit.
Police said security forces overnight detained 3,115 more people, claiming 26 of them being militants, as part of the nationwide anti-militant drive aimed at stopping the killings, taking the total number of arrests to 11,648.
"If tallied the number of people detained in the crackdown since Thursday midnight stands at 11,648. Around 145 among them are suspected militants mostly belonging to JMB," a police headquarters spokesman said.
Authorities in Bangladesh are under mounting international pressure to halt the violence, which in the past three years have claimed nearly 50 people - Hindus, Chiristians and secular bloggers - many of them by machete-wielding attackers.
Prime Minister Sheikh Hasina has vowed to catch "each and every killer".
She has accused the main opposition Bangladesh Nationalist Party (BNP) and its Islamist party ally, Jamaat-e-Islami, of orchestrating the killings to destabilise the country.
However, BNP accused the government of using the crackdown to suppress political dissent.
The BNP claimed that more than 2,000 of its leaders and activists have been arrested during the anti-militancy drive.
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