The officials, including two Under Secretaries and one Section Officer, were suspended after the Home Ministry found that Naik's NGO Islamic Research Foundation's FCRA licence was renewed recently despite several ongoing probes, including one by it.
"The action against two Under Secretaries and one Section Officer was due to their negligence in clearing the renewal while a case is still pending," Minister of State for Home Kiren Rijiju tweeted.
Mumbai Police is also probing allegations against Naik.
Naik is accused of radicalisation of youths into terror and receiving foreign funds and spending such funds in luring youths into radical views.
He came under the scanner of the security agencies after Bangladeshi newspaper 'Daily Star' reported that one of the attackers of the July 1 terror strike in Dhaka, Rohan Imtiaz, ran a propaganda on Facebook last year quoting Naik.
The popular but controversial Islamic orator is banned in the UK and Canada for his hate speech aimed against other religions. He is among 16 banned Islamic scholars in Malaysia.
He is popular in Bangladesh through his Peace TV, although his preachings often demean other religions and even other Muslim sects.
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