The astronauts assigned to crew the first flight tests and missions of the Boeing CST-100 Starliner and SpaceX Crew Dragon acknowledge the media upon introduction at NASA's Johnson Space Center in Houston, Texas, U.S., August 3, 2018. The astronauts are (L to R): Victor Glover, Robert Behnken, Michael Hopkins, Douglas Hurley, Eric Boe, Sunita Williams, Christopher Ferguson, Josh Cassada, and Nicole Mann. Richard Carson | Reuters

It's been nearly a decade since the U.S. has flown its own astronauts, a time NASA is eagerly hoping both Boeing and SpaceX will soon end. The two companies expect to launch people to space for the first time next year. But NASA will pay a significantly higher price per astronaut when flying with Boeing as opposed to SpaceX, an agency official with knowledge of the costs told CNBC on Tuesday. NASA's Office of Inspector General (OIG), the agency's auditor, said in a report last Thursday that NASA will pay $90 million to fly with Boeing – and just $55 million to fly with SpaceX. Both NASA and Boeing pushed back on OIG's report, with the company saying in a press release that it "rejects the average seat price assessment." "NASA believes the seat prices identified in the OIG report are overstated because they did not account for the cargo capability of the Boeing and SpaceX systems," NASA spokesperson Josh Finch said in a statement.

But the official who spoke to CNBC said that OIG's estimate is inline with NASA's own expectation, despite the agency and Boeing issuing public statements disputing the numbers. Additionally, neither NASA or Boeing clarified what the current set price is per astronaut. Boeing said OIG's estimate was flawed because the company "will fly the equivalent of a fifth passenger in cargo for NASA," while the auditor had only accounted for four astronauts in its analysis. NASA previously estimated it would pay $58 million to fly its astronauts with either company. But the latest numbers essentially mean it is about 60% more expensive for NASA astronauts to fly with Boeing under the current contracts than with SpaceX. Boeing and SpaceX declined CNBC's request for comment on this story, while NASA did not respond to a request for comment. The official noted that NASA anticipated Boeing to be pricier when the agency awarded the contract. SpaceX had previously won NASA funding to build and fly a cargo capsule, which Elon Musk's company used as the basis for developing the crew capsule later. While the SpaceX cargo development funding is counted under a separate NASA contract, the person noted that Boeing had to build its crew capsule largely from scratch. Since NASA wanted multiple companies to develop capsules to fly astronauts, the person said the agency expected it would have to pay a higher price to other companies that would compete with SpaceX. Under the Commercial Crew program, SpaceX and Boeing have each been developing their respective Crew Dragon and Starliner capsules. Commercial Crew is NASA's solution to once again launch U.S. astronauts from U.S. soil, as since the end of the Space Shuttle program in 2011, astronauts have flown to the International Space Station (ISS) aboard Russian Soyuz spacecraft. The OIG report in part came about as the first Commercial Crew launches have been delayed from the original target of 2017, as delays have mounted for both SpaceX and Boeing. Both companies have suffered a number of setbacks, such as Boeing's test failure of a propulsion system and SpaceX's issues with parachute testing. In the meantime, the cost per astronaut for flying with the Russians has steadily climbed, with the most recent contracts coming out to $86 million per astronaut.

SpaceX's Crew Dragon capsule splashed into the Atlantic Ocean after completing its test flight for NASA. NASA TV

OIG explains its estimate