Towing operations are highly reliant on the experience of the towing operators. Safety concerns arise when towing operations are subjected to environmental disturbances and dynamic traffic conditions. However, a systematic framework and approaches to enhance the safety and automation of towing operations remain lacking. This work proposes a framework of collision prevention of ship towing operations under environmental disturbance in near port waters. The focus is to prevent internal collisions between tug and assisted ship and provide early warning of possible collisions with other surrounding ships. A cooperative multi-agent control strategy is employed to specify the direction and magnitude of the towing force of the two tugs in real-time. Therefore, in the presence of environmental disturbance, the assisted ship can sail along the planned trajectory, and the acceptable safe geometric distance between each ship pair in the towing system is guaranteed. Further, a COLREGs-compliant collision alert system is designed to promptly remind the towing operators of a collision hazard with nearby ships, and different alert levels indicate different action obligations of towing operators. This proposed framework and developed methods are applied to a tandem towing system consisting of two tugs and one assisted ship to test its feasibility.