Her remarks came during a meeting with Japan's State Minister of Foreign Affairs Seiji Kihara at her official residence Ganabhaban.
"Describing the terror attack at Gulshan cafe as unfortunate, The Prime Minister said we must find out the roots of the culprits who supplied weapons and explosives to the terrorists for the barbaric attack," Ihsanul Karim, press secretary to the PM, told the media after the meeting.
Six of the seven Japanese killed in the terror strike were surveyors for Dhaka's Metrorail project.
The Japanese government has sent the minister to Dhaka after the attack.
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The assailants killed two police officers, who tried to enter the cafe, to break the siege.
Army commandos stormed the eatery yesterday and rescued 13 hostages, killing six attackers while capturing one alive.
The Army said 20 people were found dead on the premises during the raid, all possibly slaughtered late on Friday, hours before the commandos raided the cafe.