The samples will be sent to a forensic laboratory for confirmatory tests, SHO of Aravali Vihar police station Shishram Meena said.
The self-styled godman was arrested on Saturday by the Alwar Police after a 21-year-old women from Chhattisgarh, whose parents were his followers, filed a rape complaint earlier this month.
The woman, whose parents have been followers of Falahari Baba for years, has alleged that she was assaulted at his lavish ashram in Rajasthan's Alwar on August 7. She was allegedly told that the Baba couldn't meet anyone during an "eclipse" and asked to stay the night. The woman has told the police that the Baba called her at night to his room and assaulted her.
Warned against telling anyone, the woman broke her silence when another high profile guru, Gurmeet Ram Rahim Singh, was facing rape charges in court. Ram Rahim is now serving a 20-year jail term for raping two followers.
Facing allegations of sexual assault, the self-styled Godman had checked himself into a private hospital in Alwar earlier this week saying he was suffering from high blood pressure. On Saturday, the police got a medical examination conducted on him at a government hospital in Alwar where his sugar and blood pressure were found to be normal, following which he was arrested.
Kaushlendra Prapannacharya Falahari Maharaj, 70, is dubbed "Falahari" because of his reported fruits-only diet.
His judicial remand will end on October 6, he said.
(With inputs from PTI)