A container tracking system comprising a mobile unit configured to be coupled to a container to be tracked and to communicate with a remote control unit through of a communication system. The mobile unit comprising a positioning module, an alarm module adapted to detect alarm conditions related to said container, and a communication module generating a tracking signal containing positioning data of the mobile unit and/or alarm information associated with one or more alarm conditions related to the container. Furthermore, the mobile unit is configured to evolve to a temporary deactivation state whenever a communication unavailability condition of the tracking signal through the communication system occurs.