Most traditional vehicular Radio Frequency Identification (RFID) authentication systems combine physical tag detection with identity verification, creating security vulnerabilities such as cloning, replay, and workflow bypass attacks in sensitive border applications. This paper proposes a Lightweight Multi-Stage RFID Authentication (LMRA) protocol that enforces chronological consistency alongside credential validity using a five-stage finite state machine. Empirical testing within an eight-stage intelligent customs process demonstrated deterministic detection of all simulated threat scenarios with zero false positives and zero false negatives. An indexed primary-key query combined with an in-memory session hash table provides O(1) computational complexity, supporting scalability regardless of the number of registered records. Furthermore, an asynchronous audit engine generates unique, threat-specific non-repudiation logs without adding real-time operational latency. The results demonstrate that LMRA provides a lightweight, stage-aware, secure, and scalable authentication approach for intelligent customs checkpoints and international supply-chain logistics.