The violence on January 1 had left one person dead.
A bench headed by Justice Kurain Joseph granted Ekbote interim protection from arrest till February 20 in the case.
The apex court also sought a response from the Maharashtra government on his plea for anticipatory bail.
The apex court asked the Maharashtra government to apprise it about the law and order situation in the state.
It said that in the event of Ekbote's arrest, he should be released on bail on furnishing a bond of Rs 1 lakh.
According to the police, a court in Pune yesterday issued an arrest warrant against right-wing leader Ekbote, who was booked for allegedly inciting violence on January 1 during an event to commemorate the bicentenary of the Bhima-Koregaon battle.
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 had on February 2 rejected Ekbote's anticipatory bail plea. Before that, a Pune court had also rejected his similar plea.
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