An apparatus and method using a program protection engineering (P2E) toolkit to provide program protection engineering, security management, and report preparation for sensitive and classified projects. The P2E toolkit is an implementation of security policies, procedures, and methodologies associated with acquisition programs. Acquisition programs may range from large-scale classified systems for the government to sensitive corporate acquisition programs focusing on company proprietary or intellectual property issues. Specifically, the P2E toolkit provides end-to-end program protection engineering, security management, and report preparation for sensitive and classified programs throughout the program lifecycle, and assists security professionals and program managers to make appropriate decisions to protect their acquisition programs from compromise due to foreign intelligence threats or corporate/industrial espionage. The P2E toolkit enhances the traditional program management concerns of technical performance, schedule, and cost, by adding lifecycle protection as in integral component.