An inspection system provides for inspection of cargo containers. A scanning tunnel has an entrance and an exit, a plurality of scanning entrance doors, each having an open position and a closed position, at least one of the plurality of scanning entrance doors interior to the scanning tunnel; a plurality of scanning exit doors, each having an open position and a closed position, at least one of the plurality of scanning exit doors interior to the scanning tunnel. A scanner is adapted to scan the contents of a container inside the scanning tunnel when at least one of the plurality of scanning entrance doors is in the closed position and at least one of the plurality of scanning exit doors is in the closed position. A carrier carries the container through the tunnel.