The charges were filed at Gulshan Police Station at midnight, Inspector General of Police (IGP) AKM Shahidul Haque said.
"We filed the case under the Anti-terrorism Act...Five men have been made accused by their name and several others as unidentified accused," the duty officer of the police station said.
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Islamic State has claimed responsibility for the killing of the 20 hostages and two police officers during the 12-hour siege that ended after the army stormed the Holey Artisan Bakery popular with expats in the diplomatic zone here, killing six attackers and capturing one alive.
Hostages who were killed include 19-year-old Indian girl Tarishi Jain. Nine Italians, 7 Japanese, one American of Bangladeshi origin, and two Bangladeshis were also among the people who were killed.
Meanwhile, Foreign Minister A H Mahmood Ali briefed foreign diplomats stationed in Dhaka highlighting the current situation and steps taken by the government so far after the Friday's attack.
Police on Saturday night released the photos of the five militants and identified them as 'Akash', 'Bikash', 'Don', 'Bandhon' and 'Ripon'.
But, the Islamic State named the five gunmen in photos they released hours after the attack as Abu Umayer, Abu Salma, Abu Rahiq, Abu Muslim and Abu Muharib.
Regarding differences between names, the police chief cited the trend among militants to use aliases.
Three other gunmen were all from well-to-do families and studied ar Dhaka's top English medium schools.
However, one of the persons shown in five photos released by police was identified as Saiful Islam Chowkider, a chef at Holey Artisan Bakery.
Some of the hostage are being questioned by the police to get useful information in tracing the origins of the attack.
The Italian Foreign Ministry in travel advisories said it could not exclude the possibility of further attacks in Bangladesh.
It asked people to exercise the "utmost prudence" while travelling in Bangladesh and limit their activities to only what was necessary.
A papal Mass was held yesterday evening for the victims.
The bodies of seven Japanese nationals killed in the attack today reached home on a government plane.
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