'The spots being searched include the offices of the Tehreek-e-Hurriyat, associated with senior Hurriyat leader Syed Ali Shah Geelani, and the home of one Javed Ahmed Baba alias Gazi Baba who is also associated with the organisation.
The homes of Ayaz Akbar, a close aide of Mr Geelani and a businessman, Farooq Bagoo, were also raided.
During the searches, a few thousand rupees in Pakistani currency, and currencies belonging to the United Arab Emirates and Saudi Arabia have been seized. Several people are being questioned in this connection, said sources in the NIA.
"There is no compromise as far as the safety of the nation is concerned. Appropriate actions have been taken across or in the border. The people of Kashmir want this bluff to be called off," said union minister Jitendra Singh.
The NIA had started its investigations after a television channel aired what it said was a sting operation in which one of the members of Tehreek-e-Hurriyat, Nayeem Khan, was purportedly seen confessing to receiving money from Pakistan-based terror groups. He, however, denied making any such statement.
Last week, the NIA registered a preliminary enquiry, which was converted into a regular case over the weekend. The agency questioned Tehreek members Farooq Ahmad Dar alias 'Bitta Karate', Mr Khan and Gazi Baba. The three were asked to produce documents.
The agency conducted extensive raids yesterday on the homes and offices of separatist leaders. Searches were conducted in 14 locations in Jammu and Kashmir, seven in Delhi and one in neighbouring Haryana. So far, the agency has recovered Rs 1 crore.