"Police raided the third suspected militant den in Comilla city," a police spokesman in Dhaka told PTI.
Comilla's police chief told reporters they believe several militants with explosives were holed up inside the building.
The raid came soon after security forces came under a grenade attack as they laid a siege to hideouts of top JMB militants in separate areas of the northeastern Moulvibazar.
Top JMB leaders were said to be hiding in the buildings.
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The security forces have cordoned off the neighbourhoods.
Home Minister Asaduzzaman Khan Kamal said in Dhaka that four-five militants were likely hiding inside the building in Moulvibazar town and at least eight militants, with a huge amount of explosives, were holed up in the second building in a nearby village.
"Our plan is to evade casualties, if required army will be called out afresh," Kamal said.
Police suspect the militants stayed as tenants in the two buildings owned by one Bangladeshi-origin British national.
Earlier today, residents said they were woken up by the gunshots and grenade explosions. Authorities have enforced a cordong in the areas, barring onlookers in the vicinity.
The decision most likely was prompted after security lapses led to casualties during the Sylhet operation titled 'Twilight', when security forces killed 4 terrorists including a top leader of the neo-JMB after a four-day operation.
Six people, two of them police officers, were killed when militants hurled grenades on the onlookers during the raid.
IS has claimed several attacks in Bangladesh, but the government rejects the presence of foreign terrorist groups in the moderate Muslim-majority country, blaming homegroun groups such as the neo-JMB for terrorist attacks.
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