A cryptographic container security system for enabling the secure transportation of a container from a sender site to a receiver site. The system includes, in the exemplary embodiment, apparatuses and methods for generating pre-transportation and post-transportation fingerprints of a container being transported, for encrypting and decrypting the pre-transportation fingerprint, and for comparing pre-transportation and post-transportation fingerprints, and for comparing the decrypted pre-transportation fingerprint and the pre-transportation fingerprint. The pre-transportation and post-transportation fingerprints are generated from fingerprint data, including, without limitation, the aggregate gamma flux and aggregate effective Z-number determined for the container by multi-energy scanning systems located, respectively, at sender and receiver sites.