When installed, a web agent automatically protects the entire set of resources available on the web server. On the other hand, J2EE agents only protect resources within a web application hosted on an application server after the web application has been configured to use the J2EE agent. Thus, if multiple web applications are hosted on an application server on which a J2EE agent has been installed, only the web applications that have been specifically configured to use the J2EE agent will be protected by the agent. Other applications will remain unprotected and can potentially malfunction if they depend upon any J2EE security mechanism.
Further, the J2EE agent can only protect resources that are packaged within a web or enterprise application. Certain application servers provide an embedded web server that can be used to host non-packaged web content such as HTML files and images. Such content cannot be protected by a J2EE agent unless it is redeployed as a part of a web application.