A safety protocol was a safety plan and practice by which a process was made to be as safe as possible.
Some example safety protocols were in place for holodecks and replicators. They were often published as manuals, such as the Teratogenic Coolant Safety Protocol by A. Probert. (TNG: "Booby Trap", okudagram)
Phlox told T'Pol about the strictest safety protocols used when dealing with the industrial lubricant tetracyanate 622 due to its toxicity. (ENT: "Civilization")