The man in his 50s had participated in the construction of a plant in the southern region of Kalimantan.
When discovered on Monday, his body was dotted with wounds.
Given the condition of the site, local police believe he may have been murdered, according to the ministry.
The South Korean Embassy in Jakarta has requested that Indonesia look into the case speedily and is preparing to provide bereaved families with all necessary consular support, it added. (Yonhap)