Internet services were cut off in August 2019 when India revoked the special autonomous status enjoyed by Kashmir, broke it up into two federally administered territories and locked down the areas, imposing a communications blackout as well, according to an Al Jazeerah report.
Amnesty said it was leaving the country due to reprisals from the Hindu fundamentalist government led by Narendra Modi, adding that its bank accounts had been frozen and it had been forced to lay off staff in the country.
The human rights body said it had also been forced to suspend its campaign and research work.
Rajat Khosla, Amnesty's senior director of research, advocacy and policy, told the BBC: "We are facing a rather unprecedented situation in India. Amnesty International India has been facing an onslaught of attacks, bullying and harassment by the government in a very systematic manner.
"This is all down to the human rights work that we were doing and the government not wanting to answer questions we raised, whether it's in terms of our investigations into the Delhi riots, or the silencing of voices in Jammu and Kashmir."
Regular Internet services were restored in Kashmir in March after 213 days. India has shut down the internet more times than any other country in recent years, with more than 100 shutdowns reported last year, according to the Internet Shutdown Tracker.