As a civilian agency, NASA typically freely provides details on all aspects of its operations. The DoD shuttle missions required different procedures to maintain the secrecy of the classified payloads. The government viewed the flights and their payloads as secret as troop movements, asked media organizations to avoid reporting details, and threatened to investigate even speculation as potential leaks of classified information. The military did not disclose MSEs' names at first, unlike those chosen for Dyna-Soar and MOL, and the program's existence was secret until the press reported on it in 1982. The Air Force officially announced the MSE group's existence in 1983 but did not identify any members until 1985,and disclosed little about their role on flights.The press nonetheless reported in great detail on likely military payloads using open source intelligence, such as the direction of the shuttle after liftoff.

Unlike all other flights, NASA only began public countdowns a few minutes before launch,did not distribute press kits, and did not permit reporters to attend countdowns or listen to shuttle-to-ground communications. A secure USAF-NRO mission control center in Sunnyvale, California monitored the DoD payloads on flights alongside the Houston mission control and Firing Room 4 at Launch Control Center.NASA announced civilian shuttle missions' schedules and flight routes in advance, hundreds of civilians attended most landings, and loudspeakers played radio transmissions. Only a few reporters and NASA employees, by contrast, attended the classified flights' silent landings.