Maharashtra Chief Minister Devendra Fadnavis had yesterday asked the Mumbai Police Commissioner to conduct a probe (into Naik's speeches) and submit a report.
"As far as the Government was concerned, it will not compromise on terrorism at all", he said.
Naik is under the scanner following revelations that two of the five young militants who massacred 20 hostages, including an Indian, at a popular cafe in Bangladesh's capital Dhaka on July 1, drew their inspiration from his speeches.
He said the content of some of his speeches was being quoted out of context in doctored videos.
A senior Home Ministry official said an investigation has been ordered into the activities of IRF, which was registered under the Foreign Contribution Regulation Act (FCRA).
The Centre on Thursday had termed Naik's speeches as "highly objectionable".
He also posed a question to the ruling BJP, wondering what it would say about Sri Sri Ravi Shankar sharing the stage with Naik.
The Maharashtra government has ordered the police officials to probe all the recordings of Zakir Naik's speeches. Everything, including Naik's speeches, his social media accounts, sources of funding (of a foundation run by him in Mumbai) will be scrutinised, said Fadnavis.
"The Quran, Islam and I condemn the terrorist attack which claimed innocent lives", the Salafist preacher said in a video uploaded on his Facebook page.
"There are many scholars in Malaysia who promote peace, tolerance, moderation and true Islamic values and that these scholars should be emulated, not those like Dr Zakir", he added.
"There is not a single speech where I have encouraged one to kill another - Muslim or non-Muslim, he said".
According to reports, Areeb Majeed, who was arrested by Mumbai police upon his return to the country previous year for joining IS, admitted in front of security officials that he was inspired from the speeches of Zakir Naik.
Condemning the terror attack that took place earlier today leaving four people dead at Kishoreganj in Dhaka, Naidu said that the need of the hour for the world is to unite and not only condemn but contain terrorism.