The incident came to light this morning when one of the follower of the sect found the door of the its Mahant(head) Desh Raj alias Faquir Das (65) locked from outside, they said.
Feeling suspicious, the follower later informed the police, who broke into the room and found the victim lying in a pool of blood, they said.
Police are suspecting it to be a case of murder.
Four iron boxes, lying in his room were found broken. Later, another iron box was recovered from a field nearby, they said.
A case has been registered against unknown persons in this regard while the further probes are on, they added.