Nasa's plans to work on two new commercial spacecraft face a delay following a formal protest about the contract award process.
The complaint has been filed by an eliminated contender.
Nasa administrator Charles Bolden said the protest had been lodged by Sierra Nevada Corporation in relation to its Dreamchaser spaceplane proposal.
He was speaking in Toronto at the opening of the week-long International Astronautical Congress (IAC).
The issue will keep the agency from moving forward with the next phase of its commercial crew programme until the issue has been resolved.
Nasa has 30 days to respond and the US government accountability office is expected to issue its ruling in early January 2015.
Just two weeks ago, the US space agency awarded a $4.2bn contract to The Boeing Corporation and $2.6bn to Elon Musk's SpaceX company to pursue its space capsule designs.
Both firms must meet specified technical milestones to qualify for stage payments and have stated their seven-person crew ships could be ready to launch astronauts by late 2017.
The contracts will be used to complete design, build and test phases before flying crews on up to six operational missions to the space station 260 miles (418 km) above Earth.
They are the culmination of a four-year programme to restore US-based human spaceflight capability following the retirement of the last of the three remaining space shuttles in 2011.
Since then, Nasa has been dependent on Russia to fly its nationals to the space station, a service that currently costs the US about $70 million per seat.
Colorado-based Sierra Nevada Corporation (SNC) issued a formal protest on Friday, saying its proposal would cost $900 million less than Boeing's.
The company cited "serious questions and inconsistencies in the source selection process" as its reason for filing the legal challenge.
"SNC's filing seeks a further detailed review and evaluation of the submitted proposals and capabilities," the company said in a statement .
"SNC takes the nation's human spaceflight capability and taxpayer's money very seriously. SNC believes the result of further evaluation of the proposals submitted will be that America ends up with a more capable vehicle, at a much lower cost, with a robust and sustainable future."
The company described its Dream Chaser design as offering a wider range of capabilities and value, including "preserving the heritage" of the space shuttle programme through its design as a piloted, reusable, lifting-body spacecraft.
Its ship looks more like a mini space shuttle than a conical capsule and - like the space shuttle - would glide back to Earth to land on a runway.
Bolden said the protest precluded him from making any kind of further comment as to why the Dream Chaser proposal was not selected.