Local media quoted police as saying a man broke into the Kyoto Animation Co studio on Thursday morning and sprayed an unidentified liquid around.
Some 30 people still remain unaccounted for.
The suspect, an unidentified man, has been detained and was taken to hospital with injuries.
The fire broke out at the three-storey building at around 10:30 local time on Thursday. Rescue operations are still ongoing.
The man had been heard saying "drop dead" as he set fire to the building.
It is not clear what relationship the suspect may have had to the company.
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