India's Hindu nationalist government on Thursday ordered major universities to prominently display the country's flag at a time when it is struggling to contain the largest nationwide student protests in a quarter of a century, officials said.

All 46 centrally-funded universities have agreed to display the flags after a meeting chaired by Education Minister Smriti Irani, the government said in a statement.

The universities have been asked to install flag masts 207 feet tall - about the same height as the Statue of Liberty - to hoist the nation's tricolour flag, according to officials at India's education ministry.

"At a central place at every university, the national flag will be flown prominently and proudly," the statement said.

The flag masts will be the same size as one installed in the centre of New Delhi two years ago. The flag, weighing 35 kilograms and 90 feet long, was the largest in India at the time.

The decree follows angry demonstrations across university campuses this week after a student was arrested for sedition. Protesters accuse the government of attempting to muzzle free speech.

Kanhaiya Kumar, head of the student union at Delhi's Jawaharlal Nehru University, was arrested after attending a rally to commemorate the anniversary of the execution of Kashmiri separatist last week.

The student's detention under colonial-era laws, once used by British rulers to jail nationalist heroes such as Mahatma Gandhi, has exposed deep ideological differences about freedom of speech in India.

The police and government say the student's jailing is right because his behaviour was anti-India.

But his arrest has become a cause celebre among opposition parties who complain India is increasingly intolerant under Prime Minister Narendra Modi, who was elected in 2014.

The largest student protests have taken place at Jawaharlal Nehru University, an institution that will have to display the new flag because it is centrally funded.

"This is psychological warfare," said N. Bhaskara Rao, chairman of the Centre for Media Studies in New Delhi. "The government has decided that students are not patriotic enough and they will do something about it."