"We can see three dead bodies here, Tamim Chowdhury is dead. He is the Gulshan attack mastermind and the leader of JMB (Jamayetul Mujahideen Bangladesh)," senior police officer Sanwar Hossain said.
Chowdhury, a Bangladeshi-Canadian citizen, had earlier been named by police as the suspected mastermind of the attack on the cafe in Gulshan, an upscale Dhaka neighbourhood.
Chowdhury, with alleged Islamic State links, was killed in a three-storeyed house in Paikpara Baro Masjid area of Narayanganj.
Inspector General of police, A.K.M. Shahidul Hoque, and counter-terrorism unit chief Monirul Islam confirmed the death of Tamim Chowdhury after the raid, code-named "Operation Hit Strong 27".
A joint team of security forces, including counter-terrorism forces and the Rapid Action Battalion (RAB), had cordoned off the building around 9.36 a.m. and the operation lasted an hour.
According to police officials, a team of counter terrorism and transnational unit conducted the operation in plainclothes.
There was heavy exchange of gunfire and the militants also lobbed some grenades at the security forces. After the operation, police entered the house and found three bodies, the police said.
The raid was carried out on information extracted from one of those arrested following the July 1 attack on the Holey Artisan Bakery in Gulshan area, police sources said.
The IGP said law enforcers had given the militants scope to surrender but they did not do it, and instead opened fire and hurled grenades.
Police confirmed the identity of one of the three dead as Tamim after matching photos, the IGP said.
The other two militants killed in Saturday's raid were identified as Manik, 35, and Iqbal 25.
Tamim, who was believed to be the local coordinator for the Islamic State in Bangladesh was a high-ranking member of the local militant group called the "New Jama'atul Mujahideen Bangladesh".
According to investigators, he had accompanied the five Holey Artisan Bakery attackers from their Bashundhara flat to Gulshan, Dhaka, and left the area after bidding them farewell just before the caf? siege began on July 1, the Daily Star reported.
The five militants, carrying weapons including semi-automatic rifles, grenades and machetes, held diners hostage in the eatery in the diplomatic zone.
The militants killed 20 hostages, including 17 foreigners, and two policemen in the worst-ever terror incident in Bangladesh.
Besides his involvement in the Sholakia terror attack on July 7, in which four people were killed in a machete attack, Tamim was also believed to have been the mentor of the group of nine militants, killed in a police operation at Kalyanpur on July 26.
He used to frequent their flat in Kalyanpur and have meetings with them, give motivational speeches and guide them on planning militant attacks, according to a statement in a case filed following the police operation named "Storm 26", the Daily Star said.
Police had announced two million Bangladeshi Taka reward earlier this month for information leading to Tamim's arrest.
Tamim's name came up on the list of 10 missing people released by police after it emerged that the cafe killers and Sholakia attackers had been reported missing by their families.
Tamim lived in Windsor, Canada from where he returned to Bangladesh on October 5, 2013.
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