"I don't think I can ever feel completely safe, either in the girls' hostel or on campus," said Nayla Khwaja, a student at New Delhi's renowned Jamia Millia Islamia university.
Last month police smashed their way into the institution, firing tear gas shells as scores of terrified students barricaded doors and hid inside bathrooms.
Weeks on from the violence, large parts of the college remain deserted, with some parents refusing to allow students who flock to the university from all parts of India to return.
Less than half of the 20,000-strong student population is back on campus for the new semester, according to college chief proctor Waseem Ahmad Khan.
Beyond the capital, protests have also erupted in colleges in Mumbai, Bengaluru, Kolkata and Chennai.
In some cases they have spilled into nearby town squares, with citizens holding Indian flags and demanding the revocation of the law in the most sustained opposition to Modi since he first swept to power in 2014.
Students say they are concerned about further attacks which they blame on right-wing groups tied to the ruling Hindu nationalists.
"There is an environment of fear that was never seen before," said Saheb Samanta, a PHD scholar in Kolkata's Jadavpur University.
Students have taken to sharing live locations on WhatsApp with friends when attending a protest or going to class so they know who is where, a dozen students enrolled in universities in Delhi, Bengaluru and Kolkata told Reuters.
"We are keeping some basic checks in place. Letting friends know where we are and also sometimes walking in groups within campus. This really wasn't necessary before," said a masters student at Jadavpur University.
Like others who described the extra precautions, she declined to give her name out of concern for her safety.
DEEP ANXIETY AMONG MUSLIMS
Critics say that Modi's ruling Bharatiya Janata Party (BJP) government is targeting universities to snuff out dissent before the opposition to his policies gets out of hand.
BJP spokesman Tom Vadakkan rejected the allegation and said rival political parties were trying to use students as a way to settle political scores with it.
"These parties are trying to stay relevant," he said.
The citizenship law lays out a path to Indian nationality for six religious groups from neighbouring countries but not Muslims, prompting criticism it undermines the country's secular ethos.
It came months after the government withdrew the special status of Muslim-majority Kashmir and also after the country's top court ruled in favour of Hindus in a decades-old dispute over a place of worship that the ruling party has long campaigned for.
Such moves have stirred deep anxiety among India's Muslim population and liberals that Modi is promoting a Hindu-first agenda in a country that celebrated its rich diversity.
But the government has said the citizenship law is aimed at helping minorities like Hindus, Christians and Sikhs who face persecution in Pakistan, Afghanistan and Bangladesh.
Even small colleges in cities like Bengaluru, far from the centre of the protests in the capital, have been caught up in the unrest. Some government supporters accuse anyone opposing the citizenship law as anti-national.
This month, a group of 15 men showed up at the gates of Jyoti Nivas, a small all-women's college, demanding students sign up a charter supporting the citizenship law.
They held a banner with a picture of Modi and insisted women show support for the law.
"We said they can't force us to sign because we are not for the CAA ( citizenship amendment act)," said Soorya, a 21-year-old student who did not want to share her last name.
There was an altercation and college authorities ordered classes to be suspended for the next two days.
(Reporting by Nivedita Bhattacharjee in Bengaluru and Aftab Ahmed in New Delhi, additional reporting by Derek Francis; Editing by Sanjeev Miglani and Mike Collett-White) ((Nivedita.Bhattacharjee@thomsonreuters.com; Mobile: +91 9920455129; Office: 08067491310;))