The agency, which registered a case in September last year, filed the chargesheet against Mohammed Parvez before a designated NIA court.
The allegations are that accused had sent obscene and morphed WhatsApp images and messages from a mobile phone and Facebook ID with a veiled threat to circulate them on social media, to the complainant, thereby causing mental harassment to her as well as threatening to ruin her reputation.
"This was done in pursuance of a deep-rooted conspiracy hatched by Pakistani Intelligence officials and the arrested accused (Parvez) with a view to compromise an officer of the Indian Army into divulging national security secrets," an NIA spokesman said.
The chargesheet has been filed against accused 43-year-old Pervez, a resident of walled Delhi, under various sections of Indian Penal Code, Information Technology Act and anti-terror law UAPA.
Parvez was arrested on September 13, 2017 by the local police but after it was found that he had visited Pakistan a few times, the matter was transferred to the Special Cell for probe. The NIA took over the case later.
A woman colonel filed a police complaint in Dwarka, alleging that she had been receiving morphed and obscene pictures through WhatsApp from two unknown numbers.
After she blocked the two numbers, the woman colonel's daughter started receiving morphed pictures and messages from the Facebook profile of a woman, they said.
The person sending the pictures and messages asked the woman's daughter to speak to the sender and threatened her with uploading the pictures on social media.
The woman colonel approached the police and a case was registered. On the basis of the information gained through the Facebook profile and the records of the two numbers, Parvez was arrested.
During his interrogation, it emerged that he had visited Pakistan and had made SIM cards available to some Pakistani nationals. It was suspected that he is linked with the ISI.