In its 4,000-page chargesheet filed in a special court in Mumbai against the 51-year-old fugitive, the NIA said Naik promoted enmity and hatred between different religious groups in India through his public speeches and lectures.
He has been charged under relevant sections of the Indian Penal Code and the Unlawful Activities (Prevention) Act, an NIA release said.
"We first moved the court seeking permission to file a chargesheet and after the court's nod we filed the charge sheet," NIA prosecutor Anand Sukhdeve told reporters outside the court.
He submitted in the court that investigation against Naik was over.
The televangelist, currently abroad, was probed by the NIA for terror activities.
Naik came under the lens of security agencies after terrorists allegedly involved in the attack on a cafe in Dhaka last year reportedly claimed they were inspired by his speeches. He fled from India on July 1, 2016.
Naik was declared a proclaimed offender by the NIA court on July 21 as he did not appear before the investigating agency even after several summonses were issued.
The chargesheet noted that Naik was the founding trustee and member of the Islamic Research Foundation (IRF) and 'has been promoting enmity and hatred between different religious groups in India through his public speeches and lectures', the NIA release said.
He 'conspired with IRF Trust and Harmony Media Private Limited (both promoted by him) to commit offences of promoting hatred and outraging religious feelings,' it said.
The NIA, on November 18, 2016, registered a case against him at its Mumbai branch under the anti-terror act UAPA.
Mumbai-based IRF has already been declared an 'unlawful association' by the Union home ministry.
Opposing the NIA submissions, Naik's lawyers Mubin Solkar and Amin Solkar said that a charge sheet cannot be filed if there is only one accused who is absconding.
Special Court Judge V P Avhad said the court may look into this aspect at a later stage.
"The chargesheet runs into about 4,000 pages and names three accused -- Naik and (his organisations) IRF and Harmony Media," an NIA official said.
It contains statements of 150 witnesses including some recorded before a magistrate, the official said. These statements, unlike those recorded by the police, are admissible in court.
Naik's incriminating public speeches/uttering are still in circulation through CD/DVD and web portals, social media such as Facebook and YouTube, the NIA said.
Harmony Media shot videos of his speeches and distributed them to general public and also to Global Broadcast Corporation (in Dubai) for broadcast on Naik's Peace TV, the agency said.
Many of these incriminating speeches were delivered during peace conferences organised by the IRF in Mumbai every year during 2007 to 2011, 'where there was open exhortation to convert people of other religion into Islamic religion by Zakir Naik', the NIA said.
In his speeches, Naik 'deliberately and maliciously insulted the religious beliefs of Hindus, Christians and non-Wahabi Muslims, particularly Shia, Sufi, and Barelwis, with intention of outraging their religious feelings, and IRF and HMPL have been instrumental in the maximum circulation of such incriminating speeches', the NIA said.
Nine speeches in particular were found to be inflammatory as they hurt the religious sentiments besides inciting violence, it said.
Two statements of Naik, made during Ganapati festival in 2012, hurt the religious sentiments of the Hindus, it said.
Peace TV also violated the Communications Act, 2003 in the United Kingdom, because in presenting his theological views, Naik did not include any reference to alternative interpretations by Muslim scholars, nor did he seek to mitigate the potential offence by providing sufficient context for his remarks, as is required under the British law, the NIA release said.
The IRF and the IRF Educational Trust received huge donations from within India and abroad and most of the donation receipts showed only 'well wisher' instead of the actual name of the donor, the charge sheet said.
Nailah Naushad Noorani, Naik's sister, was a trustee of the IRF Educational Trust, and when Naik left India in 2013, he appointed her as a director in Harmony Media.
"It was found that she was director on paper only; all the affairs of companies were handled by her brother....she had received Rs 29 crore from Zakir Naik through her parents' bank account between 2013 and 2016," the NIA said.
This money was invested in Harmony Media and Longlast Constructions company as per Naik's instructions, it said.
Huge funds were received by domestic and foreign entities and individuals related to Naik, and 'huge quantity of cash has been generated in the system by entities and individuals connected to Zakir Naik which has been invested in real estate and holding companies', it said.
"The investigation has revealed that there are 19 immovable properties, including land and building, worth Rs 104 crore connected with the accused Zakir Naik. The source as well as the mode of acquisition of these properties is being investigated," the agency said.
The Enforcement Directorate has also registered a criminal case against Naik and others.
Why Zakir Naik is dangerous
What Zakir Naik and his version of Islam is about
Decoding Zakir Naik: A TV preacher or a threat?
'Islam is not a magic potion'
'Modi must say Zakir Naik is spreading hatred'