Bhola Nath, a resident of Jaipur in Rajasthan, was booked yesterday, police said.
The police had started a probe into the Nath's allegations after a court's directions four days ago.
According to the police, during the course of the trial they picked up a youth, Vikrant Sharma.
Sharma told police that Bhola had asked him to arrange skeletons of three children and get them buried inside the premises.
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Earlier, a compliant was filed before the court by a one Raj Kumar here that three children were murdered and buried inside Asaram's Bhagwati Nagar ashram.
Kumar had approached the court after hearing the statement given by Bhola on a TV channel.
The court had then directed the police to register a case and start investigations into the complaint.
Now, a police team is being deputed to arrest Bhola and bring him to Jammu for investigations, they added.
Earlier in 2008, two minor boys were found dead under mysterious circumstances near Asaram's Ahmedabad ashram.