"It was alleged that the provision of the Foreign Contribution (Regulation) Act 2010 and Indian Penal Code were contravened," the federal agency, known as the CBI, said in a statement, adding that the Indian arm received contributions from Amnesty International UK despite government restrictions.
The raids were conducted at Amnesty International's offices in Bengaluru and New Delhi after the CBI registered a case against the group based on a complaint from India's Home Ministry, the statement added.
Amnesty, which has criticised some actions of Prime Minister Narendra Modi's Hindu nationalist government in the past, was also accused of violations of foreign funding rules last year.
#LetKashmirSpeak: Sign Amnesty International's petition to end draconian IOK lockdown
"Over the past year, a pattern of harassment has emerged every time Amnesty International India stands up and speaks out against human rights violations in India," the group said in a statement.
Over 5 ED officials raided Amnesty’s Bengaluru office. Ordered employees to not leave, shut their laptops and searched their desks. Employees were not allowed to use their phones to call friends and families. #CrackdownOnAmnesty
— Amnesty India (@AIIndia) October 25, 2018
Amnesty accused Modi's government of violations of human rights in Kashmir after it revoked the constitutional autonomy of the disputed state in August and came down heavily on protesters in the aftermath.
The rights group also criticised the government's recent move to revoke the overseas Indian citizenship of British writer Aatish Taseer, calling it "discrimination based on gender and ethnic or national origin".
India has tightened surveillance of non-profit organisations in the country since Modi took power in 2014, with thousands of civil society groups having their licences to receive foreign donations cancelled or suspended.
India's financial crime investigating agency, the Enforcement Directorate (ED), froze bank accounts of environmental watchdog Greenpeace India last year, forcing the organisation to cut its staff to a bare minimum. Amnesty International's bank accounts were also frozen by the ED last year.
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