The complainant - a teen from the Rajasthan town - has accused the 72-year-old self-styled godman of sexually assaulting her at his ashram earlier this month.
The victim told Delhi's Kamla Market police that the guru had called her for a religious ceremony at his Jodhpur ashram, where he allegedly assaulted her sexually.
"We registered the complaint, but the girl said the incident occurred in Rajasthan, so the case will be forwarded to Rajasthan," a police officer said.
According to police sources, the girl told her parents, who were staunch supporters of the guru, about her ordeal on August 17 and they approached the police two days later.
The police sent her to Lok Nayak Jai Prakash Narayan Hospital for medical examination where sexual assault on the girl was confirmed.
Late in the evening, Jodhpur police filed an FIR against Asaram Bapu in which charges of rape and wrongful confinement have been levelled. Police officers visited the Jodhpur ashram in course of investigation.
In Ahmedabad, Asaram Bapu in his evening discourse for devotees, described the charges of rape as false and baseless. He said it was a conspiracy against him. Media was barred from attending the discourse.
Speaking to his devotees, Asaram bapu said "nothing has been found in the minor girl's medical report. After the infamous Damini gangrape case, Delhi police has been asked to file FIR for rape complaints immediately. The girl's parents want the investigation to continue in Delhi. The charges are false and baseless."
In Jodhpur, the local DCP Ajay Pal Lamba said, the girl who studies in class 12 in Uttar Pradesh has accused Asaram Bapu of sexual assault. "She had been studying in the gurukul for the last four years, and her parents were told to ask their daughter to undertake a special treatment from the godman. Asaram was in Jodhpur in course of a satsang 10 days ago, he made her stay in his cottage located in a deserted place and took her for treatment at night, says the girl", the DCP said.
The police official said, the baba then sexually exploited her, and then left Jodhpur before asking her parents to bring the girl to Ahmedabad. The parents then approached the police.
"Being a sensitive case, we have handed this case to a female police officer and we will take action once the investigation is complete", the DCP said.
The girl and her parents are now in Jodhpur, and they are being questioned by police.
Asaram Bapu, who has a large following, was earlier in the news after Gujarat Police filed a case of attempted murder against him and two others. He was also accused of illegal land-grabbing in Gujarat and Madhya Pradesh.
After the Dec 16, 2012 gang-rape of a 23-year-old student in a Delhi bus, Asaram Bapu attracted much attention for his remark that the victim could have escaped rape if she had called her attackers brothers, and pleaded to be let off.
"We registered the complaint. But the girl said the incident occurred in Rajasthan, so the case will be forwarded to Rajasthan," a Delhi police officer told IANS.
The complainant said the assault took place Aug 15 at a Jodhpur ashram where the girl had gone for treatment, police said.
"The girl was studying in a gurukul run by (Asaram Bapu) in Madhya Pradesh's Chhindwara district for five years. As she was not feeling well, the gurukul staff told her to visit Bapu (Asaram)," said the official.
A spokesman for the spiritual leader, who enjoys a wide following across the country and abroad, said this was an attempt to malign Asaram Bapu's image.
"The girl says the incident took place on Aug 15 at Jodhpur. But Asaram Bapu left Jodhpur on Aug 11," spokesman Sunil Wankhede told IANS on telephone from Ahmedabad. "So how could this be true?"
He added: "The girl registered the case in Delhi because Delhi is one place where police are bound to register an FIR of cases related to crime against women even without any investigation.
"We will take legal action against the girl."
The girl, a native of Uttar Pradesh's Shahjahanpur district, visited Asaram Bapu along with her family.
Police said Asaram took the girl to a separate room on the pretext of treating her illness and sexually assaulted her.
Traumatised, the girl kept mum but finally broke down a couple of days later.
The livid family members decided to confront Asaram and reached Delhi's Ramlila Maidan Tuesday where he was giving a public sermon. But the family was not allowed to meet him and instead told to leave, said police.
The family then went to police.