Four members of PFI were arrested from Phulwarisharif during a raid conducted by Patna police following intelligence inputs from the central investigating agency in July last year.
The raids were conducted following inputs that a few leaders were still actively coordinating the functioning of the PFI despite the ban.
NIA sources said the crackdown is a part of the ongoing investigations that revealed that such criminal acts were not isolated incidents.
Four PFI activists were also arrested from Kerala's Kottayam district and one from Kollam in Kerala for allegedly engaging in violent activities during the state-wide hartal on September 23.
Other senior officials, including Coimbatore City police commissioner V Balakrishnan and Coimbatore rural SP V Badrinarayanan took part in the meeting.
Stones were thrown at a Tamil Nadu State Transport Corporation Bus in Parassala police station limits. The hartal supporters vandalized a shop near Pothencode for not downing the shutters.
Shops mostly remained shut in the state, while incidents of forceful closure of shops were reported from various parts.
NIA, ED conduct searches across 15 states; top leaders arrested for terror funding, recruiting youth for terror acts
In old town of Kurnool city, mild tension prevailed as searches were conducted at the residence of Abdullah Wariz, who is suspected to be an SDPI activist.
They are accused of indulging in 'unlawful activities promoting enmity among communities' and 'waging a war against the country'.
The PFI claims to strive for a neo-social movement ostensibly for the empowerment of marginalised sections of India.
The raids, taking place mainly in South India, was termed by the NIA as the "largest ever" investigation process "till date".
National Security Advisor Ajit Doval, Union Home Secretary Ajay Bhalla, and Director General of NIA Dinkar Gupta were among the top officials who attended the high-level meeting.
The official said incriminating materials, including digital devices, documents, two daggers and over Rs 8.31 lakh, were seized during the operation.
Sources said that these gang members indulged in extortion, drug smuggling, and other organised criminal activities to finance their nefarious designs.
They said the three leaders were holding responsible positions in the UAPA Vyatireka Committee and people's organisations.
Prabhakar's daughter Swathi said her father had no connections with Maoists and he had informed the same to the officials in the previous inquiry also.
The NIA is following a lead based on a case registered in March against eight IS supporters who held a secret meeting in Kanakamala near Kannur.