Network security consists of primary concerns in future Internet development due to the ever increasing threats to current Internet. ProtoGENI is a federated testbed facility supporting slice-based experiments to manage, utilize, and monitor the resources for innovative network research. Security research in ProtoGENI is crucial because experiments conducted in manipulated or corruptted test environment can mislead about security mechanism's capabilities in a system. In this paper, existing ProtoGENI security mechanisms and functions are tested and analyzed through different experiments to find out the exploitable attacking loopholes. Experiments elaborate the existing functioning and security issues that can cause nonfunctional, semi non-functional or malfunctioned systems. Results indicate threats to ProtoGENI resources and run-time interactions. Cross-experiment communication in Emulab wireless nodes have the capability of assisting in verifying isolation between ProtoGENI slices. Host security is one of the security components, which can be enhanced by modifying default security settings including SSH port number and root login rights. Documentation of experiment environment, experiment design, results, and analysis including many observations is helpful to understand the basic functioning and security issues to improve the overall functioning and security of ProtoGENI.