Letters of Marque are official documents issued by a governmental organization to civilian vessels which allows them to operate as auxiliaries to the government. On Earth, Letters of Marque were historically granted to privateers, who would attack the shipping of rival nations. With the abolition of privateering on Earth, these documents instead became a way to increase the resources of Starfleet in emergencies.
While dealing with the threat of the Cardassian High Gul and his remaining elite guard, Captain Benjamin Sisko issued Letters of Marque to civilian vessels docked at Deep Space 9. This allowed these vessels to operate as Starfleet vessels, and participate in evacuating non essential personnel to Bajor. (DS9 novel: Station Rage)