The court was going to frame charges against Hardik in a sedition case registered against him in the city.
Principal sessions judge Geeta Gopi issued the bailable warrant against Hardik.
Hardik's lawyer Yashwantsinh Vala said he could not come to Surat because he had to appear at Padhadhari court in Rajkot district in another case.
However, prosecutor Nayan Sukhadwala urged the court to issue a warrant, saying the Patel quota leader had played truant on Wednesday too, and had been ordered to appear today.
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The next date of hearing is March 10.
Hardik, currently out on bail, was arrested by Surat police in October 2015 for 'sedition' for allegedly asking a fellow activist to kill the police instead of committing suicide.
He is facing a sedition case in Ahmedabad too.