The Information Ministry issued the order to cancel the Peace TV's downlink permission needed to broadcast in the country.
"Based on the Cabinet committee's decision, free-to-air TV channel Peace TV's downlink permission has been cancelled for violating downlink conditions," the ministry said in the directive.
A spokesman of Bangladesh Telecommunication Commission (BTRC) said, "Its (Peace TV) downlink permission has been cancelled in line with a information ministry's decision."
Doctor-turned Naik's speeches are believed to have inspired some of the Bangladeshi militants, who killed 22 people, mostly foreigners, at an upscale restaurant in Dhaka on July 1.
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A spokesman of the Information Ministry said copies of the circular have been sent to the Home Ministry, press information department, state-run BTV and cable operators association KOAB.
Home Minister Asaduzzaman Khan had earlier said that Bangladesh's intelligence agencies were investigating the 50-year-old Naik's possible role in the cafe attack.
Khan had said the investigators were also probing Naik's financial transactions in Bangladesh.
One of the slain attackers of the terrorist attack in Dhaka's high-security Gulshan area, the 22-year-old Rohan Imtiaz quoted Naik in a Facebook post in January this year where he urged "all Muslims to be terrorists".
The activities of Naik's Mumbai-based Islamic Research Foundation are also under the scanner of Indian Home Ministry amid allegations that funds from abroad received by it have been spent on political activities and inspiring people towards radical views.