This research is explain about the existence of the sugar industry in Indonesia which plays an important role for the Indonesian and other sectors. In PG Kebon Agung one of the most influential factors in the continuity of the production process is logistics management. Good logistics management will help mills more efficient and effective. This research focuses on the description of logistics management procedures, the effectivity of internal control systems on the procedure of managing logistics, the problems that arise in internal control systems on the procedure of managing logistics, and the alternative solutions to those problems. The type of this research is descriptive qualitative research with case study approach. Data collection is conducted using observation, interviews, and documentation. Data analysis is conducted by data collection, data reduction, data presentation, and conclusion. The result of this research shows that PG. Kebon Agung already has and uses internal control systems in logistics management. The internal control system is also effective, with the separation of functions, the determination of authorities and responsibilities, authorization, and auditing of financial and human resources that can be trusted, especially the financial section.