The body of Mahant Rajendranandpuri was last night found hanging from the ceiling while Prabhash Gautam's body was found lying in a pool of blood in two rooms of Sri Mohan Sanyas Ashram in Godhuli Puram, they said.
An iron rod and a cane were also recovered from the spot.
The incident came to light when Prabhash and a student of the ashram, Peeyush, were reported missing prompting police to reach the ashram which was found locked from inside, SP (city) Ashok Kumar said.
Forensic team has taken samples and four teams have been formed to investigate the case, he said.
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Police are yet to ascertain the whereabouts of Peeyush, the officer said.
Meanwhile, noted saints and Mahants of Vrindavan have threatened to protest if police failed to nab the accused.
"We shall be forced to adopt agitational approach if the case is not solved within a week," Mahant Fuldol Maharaj and Mahesha Nand Saraswati jointly said in the presence of over a dozen saints and Mahants.