They alleged that the administration told them their projects will not be accepted if they failed to transliterate their name, the name of the centre and topic of dissertation or thesis into Hindi.
However, JNU's Assistant Registrar (Evaluation) Sajjan Singh said the students were asked to transliterate into Hindi last year also.
"According to central government guidelines, degree certificates are issued in English and Hindi since last year," Singh told PTI.
A Tamil research scholar, Arun Kumar, whose dissertation topic is "Syntax of Tamil and Korean", alleged that he was "forced" to transliterate his name and the topic into Hindi.
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Today was the last date for submitting M.Phil dissertations and PhD thesis and the issue came to light when some non-Hindi speaking students complained of having trouble doing transliteration.
Another PhD scholar from Centre for Linguistics said it was "blatant imposition of Hindi".
"A lot of them (students) have faced harassment. We are forced to do this. Technical words cannot be transliterated," said the scholar, who is a Bengali.
"Whatever the government is trying to impose on people of this country, the JNU administration immediately tries to follow it without any discussion. This time, it's the imposition of Hindi in a central university," she said.