The leader submitted his plea before a bench led by Justice B R Gavai today after a Pune sessions court refused to grant him any interim protection from arrest last week.
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.
Subsequent protests against the incident had disrupted normal life in Mumbai.
While the police have charged Ekbote of inciting violence and attempt to murder, the accused, in his petition, has denied the charges.
He has claimed that he could not have been present at the time of the clashes as he had been under police protection at the time.
The high court is likely to hear his plea on January 31.
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