A Fleet Management System (FMS) with secured Iogistic operations is presented. The system security anchor is attained by first modifying the sensitive participating entities to make them physically clone-resistant. Novel joint-physical identification protocols are introduced to prohibit malicious fleet operations like illegal replacement of Vehicles, transported goods, drivers, predefined vehicle routes, starting point or destinations. The solution strategy is approached by networking all security-sensitive entities as Electronic Logging Device (ELD), Vehicle, drivers or goods and making them physically unique and securely identifiable. We propose for that purpose to embed the early concept of low-cost digital Secret Unknown Ciphers (SUCs) in such units to make them physically clone-resistant. The efficiency of that technique is demonstrated by introducing new protocols to create and manage joint-ELD-Vehicle clone-resistant identities. It is shown how to strictly prohibit many attacks in modern networked automated FMSs. System setup, sample generic protocols and solution scenarios are introduced to reach the targeted security levels. The secured joint-identities are shown to be highly resilient in the security analysis concluding this work. Such secured FMS are becoming very essential requirements and a “must-have” infrastructure in the emerging near future smart-vehicular-environment.