Police said the warrant for the arrest of Galagodaatte Gnanasara relates to an accusation of insulting the Koran that dates back to April 2014, months before the outbreak of deadly religious riots.
The magistrate ordered his arrest after he failed to appear for a court hearing into the matter today.
Police are also investigating more than a dozen recent complaints of incitement against Gnanasara, who went into hiding in May, after a series of arson attacks targeting Muslims.
Gnanasara's Buddhist Force or BBS is accused of instigating the hate crimes.
On Sunday, police said they had made the first arrest of a BBS member in connection with four arson attacks in a Colombo suburb.
Prime Minister Ranil Wickremesinghe vowed yesterday that he would not allow a repeat of 2014 anti-Muslim riots in which four people died and hundreds of homes were destroyed, promising tougher legislation.
With stoning and desecration of Muslim-owned places now an almost daily occurence, the government faces international criticism over its failure to tackle the violence and rein in the BBS.
Earlier this month, Western diplomats urged Sri Lanka to take action to stop the renewed outbreak of religious violence.
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