Militants hurled grenades from a hideout in Moulvibazar Sadar upazila as the law enforcers cordoned off two houses.
Gunfire and explosions have been reported from one of the houses surrounded by the security forces. Police said several top JMB leaders are hiding in the dens.
The Rapid Action Battalion (RAB) said the two houses have been cordoned off.
"RAB personnel have reached the spot. A counter-terrorism unit team from Dhaka is also there," he was quoted as saying by bdnews24.
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Counter-terrorism officer Mahibul Islam, who is on the spot, said they received inputs of the Moulvibazar houses after busting the terror dens in Chittagong's Sitakunda and Sylhet.
"The intelligence input on the house in Barhahaat was confirmed last night. Inputs for the house at Sarkarbazar (at Fatehpur village) were received early in morning," he said.
Islam said that bullets were fired and grenades were hurled at police from the house in Fatehpur Village. "The police also opened fire."
As the raids started early in the morning, power and gas supplies in the areas have been disconnected.
Police said the houses are owned by expatriates Saifur Sabbir and Atabbar Mia, who live in London.
The raid was launched hours after 'Operation Twilight' was wrapped up in Sylhet.
The four militants, including top neo-JMB leader Musa, were holed up in a building that saw powerful blasts claimed by the Islamic State that killed six people in northeastern Sylhet city in 'Operation Twilight'.
Authorities called out commandos on Saturday morning, two days after a security siege to the building.
On Saturday evening, two powerful bombs ripped through a crowd near the building, killing six people, two being police officers and injuring about 50, including two army officers.
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