The program's first test launches with crews on board were supposed to happen this year. But a recent Government Accountability report said the company's schedules "are aggressive" and that they "have set ambitious - rather than realistic - dates, only to frequently delay them."
SpaceX, the rocket company founded by Elon Musk, has also faced challenges and is working to show NASA that it has fixed a problem that caused one of its uncrewed Falcon 9 rockets to explode during fueling in 2016.
In its report, the GAO said that further delays in the program could "disrupt access to" the space station - which would be an enormous embarrassment for NASA. The space agency has been counting on Boeing and SpaceX to fly astronauts there. But the GAO said the delays could mean their spacecraft are not certified before the last flights NASA has secured for its astronauts on Russian rockets, which would keep an American presence on the station through early 2020.
In other words: Should delays persist, NASA could find itself with no way to get to the station, the orbiting laboratory that has cost NASA $100 billion to build and operate.
In a statement, NASA said that, "flying safely has always taken precedence over schedule. As our partners are finalising their systems, we're assessing remaining technical details and schedules for flight tests with and without crew."
The agency said it plans to announce an update on the test flight schedules next month.
Boeing said that it discovered the propellant leak during the emergency abort test in June at the White Sands Test Facility in New Mexico.
"The engines successfully ignited and ran for the full duration," the company said in a statement. "During engine shutdown, an anomaly occurred that resulted in a propellant leak."
The GAO report also said it was concerned about another problem with the abort system, causing it to "tumble, which could pose a threat to the crew's safety."
Boeing has said it fixed that problem, and that it would "meet or exceed all NASA requirements."