India's National Investigation Agency (NIA) said on Sunday it conducted raids at nearly five dozen places linked to banned religious organisation Jamaat-e-Islami (JeI) in Jammu and Kashmir in an alleged terrorism funding case.

The government accuses Jamaat-e-Islami of supporting militancy in Indian-controlled Kashmir, which is at the heart of decades of conflict with Muslim Pakistan.

India's main counter-terrorism arm said in a statement that members of the organisation have collected funds domestically and abroad through donations for the charity and welfare activities, but the funds were instead used for violent and secessionist activities.

"The funds raised by JeI are also being channelled to proscribed terrorist organisations such as Hizb-ul-Mujahideen, Lashkar-e-Taiba and others through well organised networks of JeI cadres," the agency said.

The agency raided premises of the association's leadership, its members and also trusts run by JeI.

The NIA also said JeI had motivated impressionable youth in Kashmir and recruited new members in Jammu and Kashmir to participate in disruptive secessionist activities.

JeI was banned by the Indian government after a militant strike in Kashmir more than two years ago, which was claimed by a Pakistan-based Islamist militant group and in which 40 Indian troops were killed when a suicide bomber rammed his car into a bus carrying para-military troops.

The JeI could not be reached for comment on Sunday. It has not previously commented on its funding but has said it had not done anything to invite the ban.