Abstract: The present invention provides a system for detecting explosives, drugs or radioactive or fissile material aboard waterborne vessels. The system includes a linear accelerator mounted on a floating platform such as a ship that directs a photon beam at a target vessel. If the target vessel contains explosives, drugs or radioactive or fissile material the photon beam will induce characteristic neutron radiation from these substances that is picked up by neutron radiation detectors mounted on the floating platform. Neutron radiation induced by the accelerator is detectable even through shielding such as lead. A floatation stabilization system supports the operation of the accelerator and detectors. A data storage system documents radiation data and corresponding identification data for the target vessel and can access a database containing the target vessels cargo manifest. Video cameras may be used to identify the target vessel.