"Around 2,000 students voted in the first half of polling," said JNUSU general secretary Satarupa Chakraborty.
The voting took place in two phases - morning and evening.
As per the UGC Notification of May 5 last year, candidates applying for M.Phil programmes will have to get a minimum of 55 per cent in Masters.
"Such a blanket and uniform qualifying marks with no relaxation for students from deprived sections is simply a recipe to kill reservations," said JNUSU president Mohit Pandey.
Last week, amidst protests by students in JNU over the criteria related to admission in Ph.Ds and M.Phil, HRD Minister Prakash Javadekar had said that he was open to meeting those who have grievances.