The swami was arrested last week and then granted bail. His supporters had clashed with a reporter and activists at a press meet before that.
The ashram was sealed as the police tried to find clues to trace Nithyananda, who disappeared after the chief minister said he should be arrested.
He first ran into trouble in 2010 when a sex tape allegedly of him with an actress aired on local channels. He was arrested on charges that include unnatural sex and was later given bail. More recently, an American woman said he had sexually exploited her for several years at his ashram.