The blasts happened at Mitsui Chemicals in Yamaguchi prefecture after workers tried to shut down part of the plant following a problem in a different sector.
The first explosion occurred at 2am local time killing a 22-year old worker and injuring 11 others. The second blast took place few hours later but did not hurt anyone.
The flames were brought under control about 15 hours after the second explosion.
Hundreds of nearby homes were damaged and at least six people injured by glass fragments, NHK reports.