As per the court's directive, the police will have to serve a notice seven days in advance before the arrest of Roy in the case.
The court also stayed the orders of Jaipur police directing Roy and executive producer Sheuli Sethi to not leave the city till investigation in the case is over.
However, it directed them to cooperate with the police in the investigation.
The petition was filed yesterday in Jaipur bench of the High Court seeking quashing of the FIR which was lodged last week by a local activist in connection with remarks of sociologist Ashis Nandy against ST, SC and OBC communities.
Roy along with Nandy is named in the FIR filed under section 506 of IPC (criminal intimidation) and the Scheduled Castes and Scheduled Tribes(Prevention of Atrocities) Act with Ashok Nagar police station last week.
"We got the relief and may leave Jaipur but will keep cooperating with the police in the course of investigation," Roy told PTI.
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"I will get my statement recorded before police today," he said.
Jaipur police directed the organisers yesterday to not leave the city till the investigation is over. The organisers had given undertaking to this effect.
Meanwhile, Additional Commissioner of Police Biju George Joseph said that he was not aware of the development.
Joseph said that the Jaipur police dispatched notice to Ashis Nandy by post.
"If the notice is not delivered to him, we will send our team," he said.
Nandy stoked a controversy with comments that people from ST, SC and OBC communities were the "most corrupt" during a session on January 26. A local activist Rajpal Meena lodged a complaint against him and the festival director.
Nandy left the city on Sunday morning.