Intermodal container monitoring is considered a major security issue in many major logistic companies and countries worldwide. Current representation of the problem, we face today, originated in 2002, right after the 9/11 attacks. Then, a new worldwide Container Security Initiative (CSI, 2002) was considered that shaped the perception of the transportation operations. Now more than 80 larger ports all over the world contribute to its further development and integration into everyday transportation operations and improve the regulations for the developing regions. Although, these new improvements allow us to feel safer and secure, constant management of transportation operations has become a very difficult problem for conventional data analysis methods and information systems. The paper deals with a proposal of a whole new concept for the improvement of the Containers Security Initiative (CSI) by virtually connecting safety, security processes and systems. A conceptual middleware approach with deployable intelligent agent modules is proposed to be used with possible scenarios and a testbed is used to test the solution. Middleware examples are visually programmed using National Instruments LabView software packages and Wireless sensor network hardware modules. An experimental software is used to evaluate he solution. This research is a contribution to the intermodal transportation and is intended to be used as a means or the development of intelligent transport systems.