An initial probe into the death has found that he was going through domestic discord, the police said, adding it was looking at the incident from various angles and would not draw any hasty conclusions.
The 50-year-old spiritual leader, whose original name was Uday Singh Deshmukh, allegedly committed suicide by shooting himself at his house here yesterday, police said.
"Strong circumstantial evidences and initial investigations clearly suggest that Bhaiyuji Maharaj shot himself dead. We don't have a speck of doubt over it," Deputy Inspector General of Police H C Mishra told reporters here.
He said it was being probed why he decided to take the extreme step.
Meanwhile, Bhaiyyu Maharaj's disciples, who are in the city, to pay their last respects demanded a CBI probe into his death alleging that he had been killed.
The Congress has already sought a CBI probe into the death.
"Initial investigation has suggested that Bhaiyyu was under stress due to the family discord. We are investigating the case and have not drawn a conclusion yet," the DIG said.
He said the revolver used in the incident has been sent for test.
Mr Mishra said they are investigating in whose name the licence for the weapon had been issued.
"His family members have told the police that the licence was issued in the name of Bhaiyyu," he said.
He said that in his "suicide note", the spiritual leader has said that he was taking the step due to stress.
Talking to PTI, Additional Director General of Police (ADG), Indore Range, Ajay Sharma said, "Domestic discord has come to light during the initial investigation into Bhaiyuji Maharaj's 'suicide', but besides this, we are conducting a detailed probe from other angles also."
"We will not jump to any conclusion in a haste," he said.
Bhaiyyu Maharaj's first wife died after suffering a heart attack in 2015. He later married Dr Ayushi Sharma, a native of Shivpuri, in 2017.
He has a daughter from his first wife.
ADG Sharma said a notepad was found in Bhaiyyu Maharaj's room in which he had purportedly written, "Somebody should be there to handle duties of family, I am leaving, too much stressed out, fed up".
The spiritual guru's family members claimed that it was his own handwriting, but the police will verify it by taking help of experts, the official said.
The latter part of the alleged suicide note went viral on the social media today, which says, "My all powers of finance, properties, bank accounts, all powers of signing authorities will be Vinayak, because I'm having trust in Vinayak. I'm writing this thing without pressure."
When asked about this note, DIG Mishra said in the suicide note, he has expressed wish that one of his trusted aides, who had been with him for the last 15 years, should be given the responsibility of his property and assets.
Reacting to a viral CCTV footage dated June 11, in which Bhaiyyu Maharaj is purportedly seen sitting with a woman in a local restaurant, the DIG said it has nothing to do with the 'suicide' according to investigations.
"He had gone there to facilitate the admission of his follower's kin into an educational institute," Mr Mishra added.
A disciple from Jalgaon in Maharashtra, Sambhaji Deshmukh, said the guru was "not a coward and could never take a step like suicide".
"We suspect that he was killed under some conspiracy and demand a CBI probe into the incident," Mr Deshmukh said.
Bhaiyyu Maharaj was very popular in Maharashtra and Madhya Pradesh because of his spiritual and social works.
He was one of the five religious leaders to whom the Shivraj Singh government in Madhya Pradesh had granted Minister of State (MoS) rank in April. However, he had refused to accept it, saying "a post holds no importance for a saint".