A case was registered against Ekbote and Sambhaji Bhide, who head the Hindu Ekta Aghadi and Shivraj Pratishthan respectively, for allegedly "inciting" violence that left a man dead near Bhima Koregaon on January 1.
Subsequent protests had disrupted normal life in Mumbai.
The Bombay High court has already rejected Ekbote's anticipatory bail plea.
"Police teams have been formed to trace Ekbote. We have told the court that he could not be found during searches. Before declaring him an absconder, there is a pre-condition and procedure... that a warrant needs to be issued.
Multiple teams have been formed to trace Ekbote.
A police official from the crime branch said Ekbote's friends, relatives and supporters were inquired.