The court of judicial magistrate first class (Margao) issued the warrant against Phadke as neither he nor his lawyer appeared before the court when the case came up for hearing this morning.
The GCA president had earlier sought exemption from personal appearance which was rejected by the court.
The case pertains to the alleged ticket scam during the India-Australia match held on April 6, 2001, at Fatorda stadium.
A case had been registered against several persons, including then GCA chief Dayanand Narvekar and Phadke, for intentionally placing orders for 29,000 tickets and complimentary passes beyond the capacity of the stadium, which was put at 27,000 spectators.
The case is now posted for hearing on August 29.