Critics also say the government is pushing a Hindu-first agenda, undermining the secular foundations of India’s democracy and raising fears among its 170 million Muslim minority.
The government denies any bias against any community.
Opposition politician Shashi Tharoor said Amnesty’s exit was a blow.
“India’s stature as a liberal democracy with free institutions, including media & civil society organisations, accounted for much of its soft power in the world. Actions like this both undermine our reputation as a democracy & vitiate our soft power,” he said on Twitter.
Amnesty said the federal financial crimes investigation agency, the Enforcement Directorate, had targeted it.
“The constant harassment by government agencies including the Enforcement Directorate is a result of our unequivocal calls for transparency in the government, more recently for accountability of the Delhi police and the Government of India regarding the grave human rights violations in Delhi riots and Jammu & Kashmir,” said Avinash Kumar, executive director of Amnesty International India.
“For a movement that has done nothing but raise its voices against injustice, this latest attack is akin to freezing dissent,” he said.