The Manual on Penal Colony procedures was a Starfleet manual regarding practices related to penal colonies.

In 2266, Captain James T. Kirk advised Lieutenant Berkley to refamiliarize himself with the manual, moments after Berkley unconfidently beamed cargo including infra-sensory drugs from the USS Enterprise to Tantalus Penal Colony in return for some research material destined for Central Bureau of Penology on Earth. Berkley agreed to consult the manual immediately, though Kirk suggested he first take the time to secure the research material. (TOS: "Dagger of the Mind")

The final draft script of the episode formats the manual's title thusly, indicating that it is a proper title, not merely a descriptor.