Polling was held in two phases -- between 9.30 am and 1 pm, and 2.30 pm and 5.30 pm.
The counting will begin later tonight.
No official figure on voter turnout was immediately available.
According to sources, in most of the centres the voter turnout in the first phase was less than 25 per cent out of total number of voters of around 8,000.
However, large queses formed outside polling centres as the second phase of voting began.
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Former JNUSU president Kanhaiya Kumar, who has been campaigning for AISF and its presidential candidate Aparajitha Raja, said that the turnout this year was very low because of various developments in the past two years.
Seven candidates in the fray for the post of the student's union president, which is currently held by the AISA in alliance with the SFI.
Presidential candidates and their respective parties took out processions, raised slogans and distributed pamphlets among voters in their last-ditch efforts to garner votes.
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