The group - which is headed by top lawyers Anand Grover and Indira Jaising - had received and misused $4.7 million in international funding, the CBI said in a statement
A legal rights group run by two of India's top lawyers Friday accused authorities of trying to intimidate and silence them after police raided their offices for alleged foreign funding violations.
Since 2014 Prime Minister Narendra Modi's government has suspended or barred nearly 10,000 non-profit groups from receiving foreign funding, accusing some of using the funds for "anti-national activities."
The Central Bureau of Investigation (CBI) said it had found "certain incriminating documents" during a search of offices belonging to the non-profit Lawyers Collective in New Delhi and Mumbai on Thursday.
The group - which is headed by top lawyers Anand Grover and Indira Jaising - had received and misused $4.7 million in international funding, the CBI said in a statement.
The agency was acting on a complaint from the home ministry that the NGO had conspired "with an intent to cheat the government of India" by siphoning off money it received from abroad.
Lawyers Collective said the raids were "nothing but a vicious means to humiliate, intimidate and silence its trustees whose fierce independence and advocacy for human rights, perturbs the political establishment of the day."
Opposition lawmakers called the CBI action the "latest in a long line of coercion and intimidation" against Jaising and Grover.
The group is the latest to face action after Modi's nationalist government launched a crackdown against foreign non-government organisations in 2014 when they assumed power.
A government intelligence report from the same year reportedly said associations were working with foreign powers to undermine India's economic growth.
Modi, re-elected in May, has criticized foreign-backed aid organizations, terming them "five-star activists."