Radio Frequency Identification (RFID) tags possess the ability to uniquely identify every individual item at low cost. This emerging RF technology is well suited for supply chain management and is expected to replace barcodes in the near future. However, unlike barcodes, these tags have an extended range in which they are allowed to be queried by a reader. This may result in different attack scenarios such as unauthorized scanning by malicious readers Therefore, a security protocol for RFID enabled supply chain is necessary to ensure the privacy and authentication between each tag, the corresponding reader and the backend server. In order to counter the evolving security issues, we propose a secure RFID based architecture for supply chain hierarchy. This architecture comprises of four different phases depicting the movement of a tagged item from source to destination. There are four different protocols supporting this architecture. Although this architecture was designed for use in supply chains, it can also be used for other RFID enabled applications by incurring minute changes.