The warrant was issued on Tuesday under Article 124(a) of the legal code, which forbid incitement of hatred or contempt against the government and carried a three-year jail sentence, the police said.
The monk, dubbed by Time magazine as "The Face of Buddhist Terror", is accused of making defamatory remarks against Myanmar's de facto leader Aung San Suu Kyi.
The police are yet to locate Wirathu, who, according to reports, was not at the Masoeyein Monastery in central Myanmar on Tuesday as he was due to appear before the governing body of the Buddhist clergy in Yangon, a day later.
The monk is known for his tirades against Muslims, including comments that sparked a wave of sectarian violence against the community in central Myanmar in 2013 and for supporting the military operation that led to over 700,000 Rohingya fleeing to neighbouring Bangladesh in 2017.
Wirathu was the most visible face of the 969 movement a Buddhist group that opposed expansion of Islam in Myanmar, and the now defunct Patriotic Association of Myanmar, whose anti-Muslim position led the government to pass several laws considered discriminatory against Muslims.
His controversial comments, which also include calling for a boycott of Muslim businesses and hailing the assassination of a Muslim lawyer close to Suu Kyi, prompted Facebook to close his account and led the Thai authorities to ban his entry into the country, where he was scheduled to deliver a sermon.
( With inputs from IANS )