SIT chief Bharati Singh confirmed his arrest and said he was taken for medical examination to the district hospital and will be produced later before the court, where it is anticipated that the SIT will seek his remand.
The arrest of Chinmayanand comes on a complaint from a 23-year-old law student who accused him of blackmail and rape in a video message posted on August 23 on social media.
The woman went missing next day and was later found in Dausa, Rajasthan.
The Supreme Court, which took suo moto cognisance of the incident, called the victim for a closed door hearing after which the court ordered the government of Uttar Pradesh to establish a Special Investigating Team (SIT) to investigate the accusations.
However, questions were being raised on the working of the SIT, which failed to arrest or question the BJP leader despite witnesses and evidences against him. Rather he was kept under house arrest at his ashram.
Earlier this week, Chinmayanand complained of 'uneasiness' and 'weakness', and was treated by a team of doctors at his ashram. He was later shifted to a hospital. Sources said on Thursday night, doctors advised him to shift to Lucknow for treatment, but Chinmayanand refused.
The law student, who studied in a college run by Chinmayanand, said in her statement that the self-proclaimed god man first got a video recording made while she was taking a bath and this was used to blackmail her. She claimed that she was raped several times by Chinmayanand, who threatened to eliminate her family if she raised her voice.
The woman bought spectacles fitted with a secret camera and made recording of their intimate moments, including one where he was getting a massage in a state of undress.
As the SIT apparently delayed action against the accused until, two days ago, the victim declared that she would commit suicide if Chinmayanand was not arrested.
The matter also turned into a major controversy with the Supreme Court intervention and the opposition accusing the Yogi Adityanath government of favouring Chinmayanand and avoiding his arrest.
( With inputs from IANS )