Internationally, waste handling on ships is regulated in Annex V of the Marine Pollution (MARPOL) regulation 1973/1978. Crews’ knowledge and competence in waste management and safety are specified in the Standards of Training, Certification, and Watchkeeping for Seafarers, Manila 2010. However, research shows that waste is still discharged into the sea, which disturbs the aesthetics and negatively impacts the marine environment, ecosystem, and people’s safety and security. This study investigates waste handling by container ship crews. Data were collected through a survey with 180 container ship crews at Tanjung Perak Port, Surabaya, Indonesia; and analysed using Structural Equation Modelling-Partial Least Square (SEM-PLS) software. The finding suggested a positive and significant impact of the crews’ roles in preventing marine pollution, at 31.5%. This finding confirms the need for a waste handling model on ships that considers safety and awareness. This study suggests improvements in ship management and crews’ awareness of waste handling aimed at environmental protection.