Police said the 41-year-old presume broke into the Kyoto Animation studio on Thursday morning and showered petroleum before touching off it.
The suspect has been kept and was taken to medical clinic with wounds.
Japan's Prime Minister Shinzo Abe said the episode was "unreasonably shocking for words" and offered sympathies.
Kyoto Animation, known as KyoAni, produces movies and realistic books and is all around respected by fans for the nature of its creations.
Onlookers portrayed an uproarious blast pursued by an inferno that quickly immersed the structure.
"I saw a few people with consumes, secured with something. They were raced to the emergency vehicle," one neighbor said.
Firemen discovered 10 of the exploited people on the stairs connecting the second floor to the rooftop and it is dreaded more individuals could even now be on the highest floor.
Japanese authorities said the unfortunate casualties were dead or "in cardio-aspiratory capture" - a plan routinely utilized in Japan for exploited people who have kicked the bucket yet whose passings have not yet been authoritatively affirmed.
Somewhere in the range of 36 individuals are in emergency clinic, some in a basic condition, reports state. Around 70 individuals were in the structure when the flame began.
Kyoto Animation, known as KyoAni, was established in 1981 and has delivered prevalent activity shows including "K-On" and "The Melancholy of Haruhi Suzumiya".
The studio additionally discharged an independent element anime A Silent Voice in 2016.
One of KyoAni's arrangement, Evergarden, was gotten by Netflix for a worldwide market.
It likewise distributes numerous well known realistic books essentially about adolescent school life.
The studio is likewise known for paying its illustrators a normal pay, breaking with the business' standard of paying per outline which is viewed as putting extraordinary weight on staff.