Authorities issued the warrant for 41-year-old Shinji Aoba related to arson and murder after the attack on Kyoto Animation on Thursday, NHK said.
Police plan to arrest Aoba, who has been hospitalised for heavy burns and was earlier airlifted by helicopter to a university hospital in nearby Osaka, once he recovers, NHK said.
Thirty-four people were killed in the fire on Thursday at the Kyoto Animation studio. Experts say the fire spread so fast not only because it was fuelled by petrol but because it was funnelled up a spiral staircase and there were no sprinklers to douse it.
Shouting "die" and screaming accusations of plagiarism sloshed what appeared to be petrol in the three-storey Kyoto Animation building on Thursday before setting it ablaze.
The man who believed to have started the fire at an animation studio in Japan's Kyoto has a criminal record, Russia's Sputnik News said, citing sources in Japan.
The report further said that that the suspect, identified as 41-year-old Shinji Aoba by the Japan Police, was indicted in 2012 for committing a robbery at a convenience store. He also served a prison sentence of three-and-a-half years, said the Russian news agency.
The suspect has a history of being treated for mental health issues and lives on welfare, the news outlet said. He is currently receiving treatment for the burns caused by the fire and will be questioned by the police.