The incident took place yesterday after the protesting students forcibly closed the main entrance to the campus.
Police said the injured persons were sent to a hospital for medico legal tests and that the two sides have filed complaints but a case is yet to be registered.
The JNU administration in a statement today appealed to the agitating students to immediately end their "forcible closure" of the north gate to the campus, following which it was opened.
"While verbally abusing me when I went to request them to keep the north gate open, some of them manhandled the security guards who tried to open the gate for commuters," the statement read.
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The Registrar said some security guards were injured and were taken to hospital.
He alleged that a student even threatened to kill a security guard.
The varsity administration also criticised the agitating students for protesting outside the UGC office at ITO and blocking road yesterday.
"All such disruptive activities by a small section of students have brought nothing but bad name to JNU," he said.