Dera Sacha Sauda chief Gurmeet Ram Rahim Singh was forced to leave Mysore for security reasons in the early hours of Monday, following protests from the Sikh community.
Police sources said that Singh, who was shifted to Bangalore under tight security, left for Delhi by the early morning flight.
There are widespread protests all over the country by the Sikh community, demanding Singh's arrest, after his security guards killed one person in Mumbai and fired at Sikh protest groups.
In Karnataka, the Sikh community staged protests at Bangalore and other parts of the state and threatened to intensify the agitation if he was not arrested.
On Sunday, the Dera chief remained inside the campus of a local unit, which was built only two months ago on the Mysore-Bangalore Highway, and held parleys with his followers.
The local police had to extend Z category security to the controversial leader.