The agreement lays out the rules for how the flights from the state of New Mexico will be integrated into US air space.
In a statement, Virgin Galactic said the deal brings it "another step closer" to commercial space flights.
The agreement with US authorities outlines how the FAA's air traffic control centre in Albuquerque, New Mexico, and the state's Spaceport Authority, will work with Virgin Galactic to make sure there is safe airspace for Virgin Galactic's space plane, the SpaceShipTwo.
Virgin Galactic, which is co-owned by Richard Branson and Abu Dhabi's Aabar Investments, also has agreements with the US state of California to allow test flights. The firm hopes to launch its first flight by the end of 2014.
A separate development this week the FAA declare that rival company SpaceX’s plans to build a spaceport in Texas would not have adverse consequences on the environment. SpaceX has proposed launching 12 rockets per year from a site near Brownsville in southern Texas. US regulators found that while the proposed site would create noise for residents of a nearby neighbourhood and alter the landscape, most other environmental impacts could be mitigated.
The firm, which was founded by entrepreneur Elon Musk, is set to unveil the latest model of its Dragon ship in the coming weeks, which is designed to ferry NASA astronauts to and from the International Space Station.