Police had a hard time removing the students, who shouted slogans against the University Grants Commission and demanded roll back of the decision to reduce the number of seats, from the road and resuming normal traffic.
The students alleged that the police "manhandled" them during the protest.
"We blocked the road as we were not allowed to meet the UGC Chairman. Police manhandled us but no one was detained," said JNU Students Union President Mohit Pandey.
The varsity had released its prospectus on Tuesday effecting seat cuts in the MPhil/PhD programmes across courses.
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"When HRD Minister Prakash Javdekar himself is accepting that the seat cut is due to non-recruitment of faculties, then why students are being punished?" the JNUSU president asked.
The students also submitted a memorandum to a UGC official.
"We demand that JNU should be allowed to uphold its institutional autonomy and prepare a robust defence of its existing MPhil and PhD admission policy along with the Nafey Committee recommendations," the memorandum stated.
"Like the students of the university, the teachers feel anger, desperation, and a sense of profound grief that university atmosphere that has given each of us so much has been so spitefully attacked from within," the JNUTA had said in a statement.