A system for authenticating articles comprising: an authentication manager for managing authentication information associated with the articles; a plurality of secure taggant reader instruments for reading machine readable taggants associated with the articles, the taggants including the authentication or related information, and an instrument configuration manager for secure on-line configuration of the instruments. Each taggant reader instrument is operable to securely process and send authentication information derived from a taggant to the authentication manager. The authentication manager uses the received authentication information to identify suspicious events. When suspicious events are detected, the instrument configuration manager is able to reconfigure at least some of the taggant reader instruments. Reconfiguration may also happen in the event of a product recall and/or taggant security compromise.