The blaze took hold following an explosion during working hours at the plant, reportedly a subsidiary of Japanese cosmetics maker Mandom Corp.
"A total of five people were killed in the fire, while 46 others were injured," Jakarta police chief Tito Karnavian told reporters.
Of the injured, more than half suffered burns to more than 70 per cent of their bodies, he added.
Police have deployed a forensics team to investigate the cause of the blast, which remains unclear, but have been unable to enter the site due to the heat.