The regulation of water transportation, in alignment with Law Number 21 of 1992 on Shipping, necessitates detailed guidelines for activities at sea. Government regulations are crucial for water transport licenses, particularly in passenger transit between regions. Licensing ensures the smooth operation of vessels, curbing undesirable incidents, and upholding passenger safety. Notably, Maluku province keenly adheres to rules and standard operating procedures (SOPs) governing passenger ship operations. A critical guideline pertains to the licensing process; Minister of Home Affairs Regulation Number 138 of 2017 specifies a maximum 5-day processing period for licensing and non-licensing services upon receiving the requisite documents. Yet, certain sea transport companies exceed this limit, diminishing passenger transit efficiency. Factors like document completion time, validation processes, and coordination between the governor and service heads influence this delay. To enhance licensing efficiency, a study is proposed, using binary logistic regression to identify significant factors affecting service duration. Variables include document completion time, document validation time, and coordination time between governors and agencies. Initial findings show that the document completion time significantly influences Maluku province’s ship operation licensing optimization, with 79.5% accuracy.