Protesters waved black flags and burned effigies of the Hindu nationalist prime minister while some students staged a nude protest outside the state government complex in the Assam capital of Guwahati.
Media reports said the nude protesters were detained while Assam student groups said police baton charged another group of activists.
Black flag protests — considered a strong insult — greeted Modi when he arrived in Guwahati on Friday night to start the tour of Assam, Arunachal Pradesh and Tripura as he prepares to call a national election.
India slaps cases against critics of plan to grant citizenship to non-Muslims
His nationalist Bharatiya Janata Party (BJP) has faced a severe backlash in the region over a proposed change to a 1955 citizenship act which would give Indian nationality to Hindus and other minorities who have fled the neighbouring Muslim countries of Afghanistan, Bangladesh and Pakistan.
Assam, a state of 33 million, has been plagued by decades of tensions between local tribal and indigenous groups and settlers from outside, including many Muslims and Hindus from nearby Bangladesh.
Modi insisted that his government will ensure that the amended law does not harm Assam and neighbouring states however.
Addressing one public rally, he said the bill, which still needs approval from India's upper chamber, was a "national commitment" to the minorities.
"The passage of the bill will ensure that those people who... love India more than their lives will be accommodated in India. It is a responsibility of India to accept those people," he said.
India extends controversial citizens register deadline
Modi said citizenship will only be granted after thorough checks on each applicant.
While groups in Assam want to block all outsiders, human rights activists have condemned the government law for not covering Muslims. They say it will be the first time religion has been a criteria for nationality in India, which is officially secular.
Last year the Assam government released the first draft of a state citizens' register that rejected four million mainly Muslim residents who were unable to prove they were living in the state before 1971, when millions fled Bangladesh's war of independence.
Modi said that his government was speeding up efforts to seal the India-Bangladesh border.
An election is expected to be called for April-May and the BJP's hopes in the northeastern states have been badly damaged by the new law, analysts said.
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