"We passed this bill to help the persecuted," he said at a rally in Delhi. "We need to respect India's MPs and its parliament".
More than 20 people have died in ten days of clashes sparked by the bill, which critics see as anti-Muslim.
Protesters have continued to take to the streets in spite of police bans.
Several thousand people have also been detained and internet services have been suspended as the authorities battle to restore order.
The bill offers amnesty to non-Muslim illegal immigrants from three neighbouring countries.
Mr Modi defended the legislation at a rally in the capital at the start of his Hindu nationalist Bharatiya Janata Party's (BJP) campaign for state elections there. The prime minister: