"Salman told the chief judicial magistrate court that he is innocent and he had been falsely implicated in the poaching case," Hastimal Saraswat, the actor's counsel, told on phone from Jodhpur.
The actor appeared with comedian Satish Shah in the court.
Salman, Shah and four others were booked by police under the Wildlife Protection Act for allegedly killing a deer and two black bucks at Ghoda farms and Bhawad in Jodhpur Oct 11, 1998.
The Mumbai High Court had on Dec 15 granted short-term relief to Salman Khan, who had sought the cancellation of a non-bailable arrest warrant issued against him by a Jodhpur court.
Thursday's hearing lasted over four hours, Saraswat said. "The arguments will continue on Friday and all the accused will be present in the court," he said.