Methods and apparatus are provided for improving message-based security in a Fibre Channel network. More specifically, the present invention relates to methods and apparatus for providing confidentiality for Fibre Channel control messages encapsulated within Common Transport Information Units. Control messages transported with the Fibre Channel Common Transport protocol, and passed between Fibre Channel network entities, can be encrypted providing confidentiality combined with data origin authentication, integrity and anti-replay protection provided by existing Fibre Channel security mechanisms.