A method and system for separating human waste solids from liquid for a shipboard toilet system that allows for the separation of solid waste, compaction of the solid waste and storage of solid waste. Wastes are deposited into a shipboard toilet system that uses vacuum toilets to flush waste into a large, inclined solid waste separation tank. A vacuum pump is attached to the separation tank to maintain negative pressure within the tank and system and to move the separated liquid stream. The separation tank has a separating screen disposed across its entire width to retain solid wastes while allowing liquid to flow through. After separation from liquids, solid waste material is compacted and dewatered with a helical screw through an inclined tube, and packaged for later removal as landfill or burned in the ship incinerator.