The formalities to file the chargesheet against Naik, who left the country in July last year, have been completed and it will be submitted before a special court this week, they said.
The 51-year-old televangelist, who is currently abroad, is being probed under terror and money-laundering charges by the NIA. He fled from India on July 1, 2016, after terrorists in neighbouring Bangladesh claimed that they were inspired by his speeches.
The NIA had on November 18, 2016, registered a case against Naik at its Mumbai branch under various sections of the Indian Penal Code and Unlawful Activities (Prevention) Act.
His Mumbai-based NGO, Islamic Research Foundation (IRF), has already been declared an unlawful association by the Union Home Ministry.
Naik is said to have acquired citizenship of Saudi Arabia but this has not been confirmed yet.
The controversial preacher has been accused of spreading hatred by his provocative speeches, funding terrorists and laundering several crores of rupees over the years.
Naik, a medical doctor-turned preacher, during his interactions with the Indian media from broad has repeatedly denied all the charges.
The Interpol was approached against Naik after a year-long probe during which the NIA gathered evidence on his IRF and Peace TV being used to allegedly promote hatred between different religious groups.
Besides banning his NGO, the central government has taken his TV channel off air.
The passport of Naik was also been revoked by the Ministry of External Affairs at the request of the NIA earlier this year.
The NIA had thrice issued notices under the Code of Criminal Procedure section 160 to Naik, asking him to join the investigation, but he did not appear before it.
The section authorises a police officer to call somebody if it appeared the person seemed to be acquainted with the facts and circumstances of the case in question.
Thereafter, on April 21, the Additional Sessions Judge presiding over the NIA Special Court had issued a non-bailable warrant against him. On June 15, the court issued proclamation order seeking Naik's appearance before it.
After Naik failed to comply with these directives, the anti-terror agency requested the Ministry of External Affairs to revoke his passport.
The Mumbai-based preacher came under the lens of security agencies after some terrorists allegedly involved in the attack on a cafe in Dhaka in July last year reportedly claimed they were inspired by his speeches.
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