It said that Saudi's King Salman 'personally intervened' to grant citizenship to Naik to 'save him from arrest by Interpol'.
On Thursday, a non-bailable warrant was issued against Naik by a special National Investigation Agency court in Mumbai . Naik is wanted by the agency for his alleged role in a terror case.
Last week, another Mumbai court had issued a NBW against Naik in a case of money laundering registered by the Enforcement Directorate.
The arrest of Naik is urgently required for the purpose of the investigation in order to unearth the entire conspiracy, the NIA said.
Naik, 51, left India last year, allegedly to evade arrest after some perpetrators of Dhaka terror attack claimed that they were inspired by him.
Following the Dhaka attack, the NIA had registered a case against him and some officials of his organisation, Islamic Research Foundation, under section 153-A (promoting enmity between different groups on grounds of religion) of the Indian Penal Code and the Unlawful Activities (Prevention) Act.
Why Zakir Naik is dangerous
Zakir Naik's allegation on TV channel wrong, says government
Zakir Naik says he will not return to India this year
IRF ban is an attack on Muslims and democracy: Zakir Naik