The case was filed against vice-chancellor Surendra Kumar at Haridwar's Kankhal police station a couple of days back by a man from Uttar Pradesh's Saharanpur.
The complainant alleged that Kumar landed this job on the basis of fake degrees.
Though Kumar denied the charges and said he is ready to face any probe, Kankhal police station SHO Ritesh Shah said they have procured his certificates from the registrar of the university concerned considering the seriousness of the charges.
Gurukul Kangdi Vishwavidyalaya is run by Arya Samaj.
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On being contacted, the V-C said it was a "conspiracy" to malign him. He attributed the "conspiracy" to the rivalry between different Arya Samaj's representative organisations based in Haryana, Punjab and Delhi.
He said he had been educated in the Guru-Shishya tradition in the ancient Ashram system of education.
No stranger to controversies, the Gurukul Kangdi Vishwavidyalaya had earlier been in the news for its land being sold to private parties and appointments allegedly being made in the university on the basis of fake degrees.