The Federation Merchant Marine can trace its origins to the Earth Cargo Service of the mid to late 22nd century. Upon the founding of the United Federation of Planets in 2161, all civilian space vessel operation was transferred to the control of the Federation Department of Transportation.
It is the Department of the Transportation which regulates space vessel operation, issues professional licenses, and enforces stellar rules of navigation.
Federation Department of Transportation
The primary operating agency of the Federation Merchant Marine, the Department of Transportation oversees the operation of all civilian freighters, cargo vessels, tankers, and transports.
United Earth Space Probe Agency (UESPA)
The original scientific space exploration arm of the United Earth, by the 23rd century the United Earth Space Probe Agency had assumed mainly an advisory role to the Federation Starfleet. The operation of civilian scientific research craft, however, has remained under UESPA control.
Starfleet Auxiliary Fleet
The Auxiliary Fleet of the Starfleet consists of military transports, hospital ships, and shuttle carriers. Manned by civilian crews in support of Starfleet missions, such vessels are maintained in lay-up until needed for an active deployment.
Planetary Merchant Fleets
Merchant vessels registered to individual planetary governments fall under the authority of the Federation Merchant Marine when transiting through interstellar space.
When conducting operations inside planetary star systems, local space regulations typically apply.
Foreign Merchant Vessels
Although not technically a part of the Federation Merchant Marine, any foreign or alien merchant craft transiting through Federation space falls under the jurisdiction of the Federation Department of Transportation.