A ban on hijab at schools has prompted an outcry among Muslims in southern India, with large crowds taking to the streets on Monday to protest against the restrictions.

The stand-off in Karnataka state has galvanised fears among the minority community about what they say is increasing persecution under the Hindu nationalist government of Prime Minister Narendra Modi.

Students at a government-run high school were told not to wear hijabs last month, an edict that soon spread to at least two other educational institutions in the state.

“It's discriminatory in nature and also it's against the rights that are provided under the constitution of India,” Sumayya Roushan, president of the Girls Islamic Organisation Karnataka, said at a Monday press conference.

Roushan said the ban violated “a personal choice that the students are entitled to, which doesn't ... harm any other person”.

Social media footage showed hundreds of people gathered on roads and waving Indian flags in at least two towns in Karnataka, the latest in several days of demonstrations held to condemn the bans.

Also read: Another college in India's Karnataka denies entry to students wearing hijab

One of the schools has since partially yielded, allowing its female Muslim students to attend class with a hijab but instructing them to sit in separate classrooms, according to local media.

Two other schools that had implemented a hijab ban declared a holiday and were closed on Monday.

Modi's right-wing Bharatiya Janata Party governs the Karnataka state and several prominent members have thrown their support behind the ban, which has been criticised by other political leaders.

“By letting students' hijab come in the way of their education, we are robbing the future of the daughters of India,” Rahul Gandhi of the opposition Congress party tweeted last week.

The state's top court is expected to hear petitions on Tuesday and rule on whether to overturn the bans.