Officials said the ministry took cognizance of reports in the media after which it directed the Registrar of the University to resolve the matter promptly and said "genuine grievances should be looked into".
It is learnt that the JNU authorities have already got in touch with the student, an official said.
The HRD Ministry has drawn flak over the suicide of Rohith, a Dalit scholar at Hyderabad Central University.
Close on the heels of the controversy, the Dalit student of JNU had reportedly sent two letters to the Vice Chancellor threatening to end his life if his research grant is not extended next year.
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Alleging that he has been "discriminated and harassed" by his department which is trying to "block his PhD", the Dalit researcher demanded resumption of his fellowship in a week's time or he would commit suicide.
In a separate letter, he contended that he was absent from the university for a certain period due to death of four members of his family, including his father and brother, and now that he has resumed his studies, he wants his fellowship to continue.