But protesters returned to the streets in Assam - one of India's remote northeastern states that had previously opposed the bill - and blocked roads, burnt tyres and painted walls with slogans against the new proposal.
Student groups called for dawn-to-dusk shutdown in four districts of the state. Shops, businesses, educational and financial institutions remained shut and public transport stayed off the roads.
"We will fight and oppose the bill till the last drop of our blood," All Assam Students' Union adviser Samujjal Bhattacharya told Reuters, underlining the region's resistance against migrants amid fears that tens of thousands of settlers from neighbouring Bangladesh would gain citizenship.
In Modi's home state of Gujarat and the eastern city of Kolkata, hundreds of people staged protests and marched against the proposed law.
In a statement issued on Monday, a group of more than 1,000 Indian scientists and scholars also called for the immediate withdrawal of the bill.
"We fear, in particular, that the careful exclusion of Muslims from the ambit of the bill will greatly strain the pluralistic fabric of the country," the statement said.
After going through the lower house of parliament, where the BJP has a majority, the bill has to be okayed by the upper house, where the ruling party does not have enough votes for passage. Any bill needs to be ratified by both houses of India's parliament to become law.
"Please save this country from this law and save the home minister," Asaduddin Owaisi, an opposition MP from the All India Majlis-e-Ittehadul Muslimeen party, told parliament.