Roy's statement came after police in New Delhi said they were weighing whether to bring sedition charges against the Booker prize-winning author over comments she made about Kashmir in recent days.
The author of the novel "The God of Small Things" issued a statement Tuesday saying her remarks urging "azadi" or freedom for Kashmir were "fundamentally a call for justice."
The region has been beset by violence, curfews and strikes since early June, when a 17-year-old student was killed by a police teargas shell. Since then, a total of 111 protesters and bystanders have died.
"What I say comes from love and pride. It comes from not wanting people to be killed, raped, imprisoned or have their finger-nails pulled out in order to force them to say they are Indians," she said in an emailed statement.
Arundhati, who has emerged in recent years as a prominent social activist, has spoken out on two occasions in recent days on Kashmir.
The Hindu nationalist Bharatiya Janata Party has objected strongly to Roy's remarks, calling them "seditious" and accusing the Congress-led government of "looking the other way" by not taking any legal action against Roy.
Law Minister Veerappa Moily said the comments were "most unfortunate". While there is freedom of speech, "it can't violate the patriotic sentiments of the people," Moily said, according to the Press Trust of India.
Nuclear-armed India and Pakistan each hold part of Kashmir but claim it in full. India insists that Kashmir is an "integral part" of the country.
The Himalayan region, which has triggered two wars between the nuclear-armed neighbours, has been wracked by a militant insurgency against Indian rule since 1989.
Rebel violence has declined sharply since the start of a peace process between India and Pakistan.
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