In a competitive business environment, RFID technology can help a business to optimize its supply chain. However, it may also enable an adversary using covert channels to surreptitiously learn sensitive information about the supply chain of a target business. We argue that the tracking of tags and the compromising of readers can create covert channels in the supply chain and cause detrimental market effects. To mitigate such attacks, we propose a framework that enables a business to monitor its supply chain in a fine-grained manner. We model the supply chain as a network flow graph, select key nodes to verify the tag flow, and actively search for covert channels. We note that optimal checkpoint node selection is NP-Complete, propose node selection and flow verification heuristics with various tradeoffs, and discuss appropriate countermeasures against covert channels detected in the supply chain. These practical methods can be implemented economically using current RFID technology.