Explaining how scuffles turned violent, it said those who had registered in the winter semester wanted to enter the school buildings but they were physically prevented by students agitating against the hostel fee hike.
The JNUSU had also called for a boycott of the registration process to press for a complete rollback of the increase in hostel fees.
Since Sunday afternoon, the varsity said in a statement, "the campus witnessed scuffles at the schools as well as inside the hostel premises between groups of students who wanted to stop the registration and those who wanted to register and continue their studies."
A group of students opposed to the registration process moved aggressively from the front of the administration block and reached the hostels around 4.30 pm. The administration immediately contacted police.
"However, by the time police came, the students who are for the registration were beaten up by a group of agitating students opposing the registration," the university added.
"Some masked miscreants also entered Periyar hostel rooms and attacked students with sticks and rods," it said, adding a few security guards were also badly injured in the clashes.
The JNU administration said it is with the students during the "difficult time".
"It is unfortunate that a group of students with their violent means of protests are preventing thousands of non-agitating students from pursuing their academic activities," it added.
JNU adminstration appeals to all the stakeholders to maintain peace on the campus.
Watch Video | JNU Violence: Video of masked goons attacking students goes viral
The registration process started on January 1 but a group of students opposed to it made the servers used in the process dysfunctional on January 3, according to the university.
This led to the discontinuation of the registration process on January 3.
A police complaint was filed immediately identifying the students.
However, on January 4 morning, the technical staff again made the CIS functional.
"Immediately, thousands of students started registering by paying the new hostel room rent. A group of students who are bent upon stopping the registration process, again entered the CIS premises with a criminal intent to make the servers dysfunctional," the varsity said.
The varsity alleged that the students damaged the power supplies, broke the optical fibres and made the servers dysfunctional again disrupting the registration process. A police complaint was again filed against the miscreants.
"For the past few days, the group of agitating students also closed the buildings of some Schools preventing the non agitating students, staff and the faculty members," the varsity said.