A very promising application of active RFID systems is the electronic seal, an electronic device to guarantee the authenticity and integrity of freight containers. To provide freight containers with a high level of tamper resistance, the security of electronic seals must be ensured. In this paper, we present the design and implementation of an electronic seal protection system. First, we propose the eSeal Protection Protocol (ePP). Next, we implement and evaluate various cryptographic primitives as building blocks for our protocol. Our experimental results show that AES-CBC-MAC achieves the best performance among various schemes for message authentication and session key derivation. Finally, we implement a new electronic seal system equipped with ePP, and evaluate its performance using a real-world platform. Our evaluation shows that ePP guarantees a sufficient performance over an ARM9-based interrogator.