The 51-year-old's passport was revoked by the Regional Passport Office of Mumbai today.
He is being probed for terror and money laundering charges by the NIA. He fled from India on July 1 last year while investigations were on over his speeches that allegedly "spread enmity" among communities, after Bangladesh said five of the terrorists involved in the attack on the Holey Artisan cafe were following his sermons.
According to 'Middle East Monitor', an online news portal on developments in Middle East, Zakir Naik has already been granted citizenship of Saudi Arabia. There was no independent verification to this so far.
Zakir Naik had his passport renewed in January last year and it has a validity for 10 years.
The NIA, on November 18, 2016, had registered a criminal case against him at its Mumbai branch under various sections of Indian Penal Code and Unlawful Activities (Prevention) Act.
His organisation, Islamic Research Foundation (IRF), has already been declared as an unlawful association by the government a day prior to registering of the case.
The sources could not give the exact country where Zakir Naik could be at present and said that he may be changing his base quite frequently after the NIA moved the Interpol for issuance of a Red Corner Notice (RCN), international arrest warrant, against him.
The Interpol was approached against Zakir Naik after a yearlong probe during which the NIA gathered evidence of his IRF and Peace TV being used to allegedly promote hatred between different religious groups.
The central government has already banned his NGO and taken his TV channel off air. During the probe, the NIA claimed to have found 37 properties owned by Mr Naik and companies run by him, which are estimated to be worth more than Rs 100 crore.
A special NIA court in Mumbai, while issuing a nonbailable warrant against Mr Naik, had said that "there are reasonable grounds to believe that Mr Naik is evading arrest and that he will not voluntarily appear before the court or before the agency."