India’s higher education crisis runs deep and wide. Teaching and learning, research, administration and student employability all suffer amid inadequate funding, corruption and excessive bureaucracy.

Recent actions by the government to address some of these issues, such as boosts to funding and autonomy for certain institutions, while inadequate in themselves, have at least created a sense that things are starting to move in the right direction. However, last month’s furore over government efforts to repress academic freedom underline that political control of India’s universities can just as easily be tightened as relaxed.

In May, the University Grants Commission, higher education’s supposedly autonomous regulator, sent a letter to India’s central universities – comprehensive institutions directly funded by the government in New Delhi – advising them that the would henceforth be applied to university teachers and researchers, rather than just administrators. The key component of these rules is that government employees cannot criticise the government or its policies.

Unlike the science-focused Indian Institutes of Technology, which are also funded from New Delhi, central universities tend to have a large variety of humanities and social science programmes, leading them to be more independent-spirited. That streak of nonconformity, even dissent, is partly why, against the odds, some of the central universities are rated among the best institutions in the country. Indeed, quite a few – Jawaharlal Nehru University and the University of Hyderabad, among others – outperform many IITs in India’s national university rankings.

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However, from the right-wing BJP government’s perspective, many central universities are troublemakers. At Jawaharlal Nehru and Hyderabad, left-wing ideas remain popular among large numbers of teachers and students, and outspoken faculty are among the most vocal critics of Narendra Modi, the prime minister.

The imposition of the CCS rules was meant to put an end to that. The rules forbid any “government servant” from making (even anonymously, and via any written or spoken media) “any statement of fact or opinion which has the effect of an adverse criticism of any current or recent policy of the central government or a State government”.

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The government’s twisted reasoning was evidently that because central universities are funded by the government, teachers should comply with the same rules on dissent as other government employees do. It overlooked the fact that this injunction constitutes a fundamental violation of the notion of independent thinking and expression: the defining feature of academia in liberal, democratic settings.

While the CCS rules would be especially harsh on those scores of academics who intervene regularly in public discussions on issues of national importance in the media, they would touch every academic who publishes in any form, whether books, journals or op-ed articles.

However, as Aditya Narain Misra, a former president of the Delhi University Teachers Association, in an op-ed, the government’s directive is in violation of a landmark judgment by the Allahabad High Court in 2015, which ruled that academics are not civil servants. So the CCS rules should, therefore, not apply to academics.

Some central universities, including the University of Delhi, had dragged their feet on implementing the government directive and even resisted it, but others adopted it. The issue came to a head when, in October, the Jawaharlal Nehru administration acceded, under a compliant vice-chancellor who had been appointed by the current government. There are that official university procedures were not followed as the changes were railroaded through.

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The backlash was immediate. Defiant Jawaharlal Nehru faculty in the press as “the most extreme form of state control of universities”. Street protests and a Twitter campaign ) were launched. And the resistance had an effect. Within 10 days or so, Jawaharlal Nehru’s executive council the CCS rules and said that it would establish a committee to reframe its own conduct guidelines. Shortly afterwards, the Ministry of Human Resource Development that enforcement of the rules was optional for academic institutions.

Nevertheless, the government’s intolerance of criticism gives good reason to fear that it may again try to “discipline” India’s outspoken academics.

Pushkar is director of The International Centre Goa.