Thousands of protestors defied Indian troops and a curfew, in violent clashes against new laws making it easier for non-Muslim minorities from neighbouring countries to seek citizenship.
At least two men were shot dead and 11 others wounded as police tried to disperse crowds in Assam with tear gas and bullets.
Protesters reportedly uprooted telephone poles, burned vehicles and also attacked the homes of officials from the governing Hindu nationalist party and the regional group Assam Gana Parishad.
Narendra Modi's Hindu nationalist government has said its Citizenship Amendment Bill is meant to protect persecuted minorities from Bangladesh, Pakistan and Afghanistan.
But thousands protested in Assam fearing it will open the gates to large numbers of migrants from neighbouring Bangladesh.
Elsewhere, the amendment has also been criticised for undermining India's secular constitution, and pushing Mr Modi's Hindu first agenda, by not offering protection to Muslims. The law passed earlier this week grants Indian nationality to Buddhists, Christians, Hindus, Jains, Parsis and Sikhs who fled Afghanistan, Bangladesh and Pakistan before 2015.
The government has said the new law will be followed by a national citizenship register that means Muslims must prove they were original residents of India and not refugees from these three countries, potentially rendering some of them stateless.
“I want to assure my brothers and sisters of Assam that they have nothing to worry after the passing of Citizenship Amendment Bill,” Mr Modi said. “I want to assure them, no one can take away your rights, unique identity and beautiful culture.”
Extra troops were deployed to restore peace and mobile internet was cut in 10 districts, the government said.
As the protests quickly turned violent, four railway stations in Assam were vandalised. Passengers and air travellers were stranded as trains and flights were cancelled due to the unrest.
Illegal immigration from Bangladesh has stirred resentment in Assam for decades.
"This is a spontaneous public outburst," said Nehal Jain, a masters student in communications in Guwahati told Reuters. "First they tell us there are too many illegal immigrants and we need to get rid of them. Then they bring in this law that would allow citizenship to immigrants."
Passing the bill was an election pledge by Mr Modi, and helped energise his Hindu nationalist support base.
Avinash Kumar, executive director of Amnesty India, said "Welcoming asylum seekers is a positive step, but in a secular country like India, slamming the door on persecuted Muslims and other communities merely for their faith reeks of fear-mongering and bigotry."
The combination of the amendment and the new register of citizens will deliberately discriminate against Muslims who cannot prove their citizenship, rights groups say.
“The amendments also set a dangerous shift in the way citizenship will be determined in India. Worryingly, they also stand to create the biggest statelessness crisis of the world causing immense human suffering,” Mr Kumar added.
Opposition parliamentarians said the bill would be challenged in court.
Yet Amit Shah, the Home Minister, rejected criticism the legislation was anti-Muslim, saying it did not affect the existing path to citizenship available to all communities.