Asaram Bapu, 72, denied any involvement in the alleged incident but could be held longer if a judge in Jodhpur agrees, police said.
Bapu was accused of sexual assault by an underage girl. His ashram outside Jodhpur was declared a crime scene by police investigators.
Asaram allegedly assaulted the victim under the pretext of performing a form of exorcism.
The Indo-Asian News Service said the guru's son has said publicly the alleged victim was mentally unstable.