A U.S. court has ordered Indian Prime Minister Narendra Modi to answer allegations that he failed to stop anti-Muslim rioting when he was chief minister of Gujarat state, overshadowing his first trip to the United States as his country's leader.

The civil case before a New York court seeks compensatory and punitive damages from Modi for crimes against humanity and extrajudicial killings under the Alien Tort Claims Act and the Torture Victim Protection Act. Modi has 21 days to respond.

The petitioner in the case is the American Justice Center, a non-profit human rights organisation, acting on behalf of two survivors of the 2002 riots in the western Indian state.

"There is evidence to support the conclusion that minister Modi committed both acts of intentional and malicious direction to authorities in India to kill and maim innocent persons of the Muslim faith," the petition said.

After years of being unwelcome in the United States, Modi will arrive for a five-day visit on Friday where he will speak at the United Nations in New York before heading to Washington for talks with President Barack Obama.

The first meeting between the two leaders follows Modi's landslide general election victory in May. Compared with other foreign powers, Washington was slow to warm to Modi, with its ambassador to India only meeting him in February when opinion polls put the Hindu nationalist leader on course to win.

Modi, 64, was denied a U.S. visa in 2005 under the terms of a 1998 U.S. law that bars entry to foreigners who have committed "particularly severe violations of religious freedom".

At least 1,000 people, most of them Muslims, died in a wave of reprisal attacks across Gujarat after a train carrying Hindu pilgrims was set on fire in February 2002.

Critics accuse Modi, who was chief minister of the state from 2001 until this year, of doing too little to stop revenge attacks on minority Muslims. He denies the accusations and was exonerated in an Indian Supreme Court inquiry in 2012.

An Indian government spokesman was not immediately available for comment, and a spokesman for Modi's Bharatiya Janata Party declined to comment.

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