In a statement on Wednesday evening, Hangloo said that he was being hounded and hence resigned under pressure.
"It is correct that I have resigned. The reason was that, repeatedly, baseless enquiries were initiated against me. On several occasions it was proved that there was no substance in the complaints. I resigned because I was totally fed up," he said in the statement.
Several complaints against Hangloo's style of functioning had been filed in the past as well.
In one such case, the National Commission of Women (NCW) had made an 'adverse' against him.
He challenged the allegations, saying: "Let the NCW prove the charges before the CBI, let them prove them before the High Court."
Hangloo however, said that he has always performed his duties in an honest manner and stood up to pressure and interference.
He further alleged the active presence of "mafia" in the university.
"There are appointments of 1,200 people to be made. If I was there, I would go on a merit basis. I will not go by mere recommendation. I will not take orders from the mafia," he added.
Hangloo said he planned to take legal recourse.
He pointed out that the President's office had twice returned the file regarding allegations against him because they did not find any merit.
NCW Chair Rekha Sharma claimed that the Commission had sent a team to the campus recently that had found grave irregularities.
She said that the "team also spoke to women in the university and mishandling of sexual harassment cases was established."
On December 26, Hangloo appeared before the NCW and denied all allegations.
Professor Hangloo was appointed as Vice Chancellor in 2015. He had earlier served as Vice Chancellor of the Kalyani University in West Bengal.
( With inputs from IANS )