"Our SWAT (Special Weapons and Tactics) team launched the assaults code-named 'Operation Hit Back' on their hideouts," district police assistant superintendent Roshunuzzaman Siddiqqui said.
Twelve militants are believed to be inside the two houses, some 20 km apart. Both the houses are owned by a Bangladeshi man living in England, police said.
Police also raided a militant hideout in Comilla municipality where at least two militants are said to be hiding with huge explosives.
Explosions and continuous firing were heard after SWAT team launched 'Operation Hit Back' at Nasirpur militant hideout in Moulvibazar Sadar upazila amid rough weather.
Cops fired tear gas shells at the house. As rain pelted down, the special team of police entered the premises of the house, which remains cordoned off by law enforcers since yesterday, police said.
During the 70-minute raid yeaterday at Nasirpur, more than 300 shots were fired but police could not confirm if any of the militants were killed.
"Law enforcers are yet to take control of the militant den in Nasirpur," Chief of Counter Terrorism and Transitional Crime unit Monirul Islam said.
The operation will take more time, Monirul said.
The SWAT team will begin next operation at Borohat in Sadar headquarter after wrapping up the Nasirpur part, he added.
Authorities have enforced a cordon in the areas, barring onlookers in the vicinity.
The decision most likely was prompted after security lapses led to casualties during the Sylhet 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 home-grown groups such as the neo-JMB for terrorist attacks.
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