Both companies have been shooting for test flights by the end of this year.
In the report, NASA said it was working closely with its commercial partners to resolve the issues and was developing contingency plans in case of further delays.
Further delays are likely as the Commercial Crew Program's schedule risk analysis shows that the certification milestone is likely to slip.
"Boeing is working with NASA to ensure that the CST-100 Starliner flies at the earliest time it is safe to do so", Boeing senior spokesman Jerry Drelling told Reuters in an email.
"NASA needs to develop a backup plan for ensuring a USA presence on the International Space Station and clarify how it will determine its risk tolerance for loss of crew", the agency said in a statement late on Wednesday.
NASA has had to rely on Russian Federation to take crews to and from the ISS on Russia's Soyuz spacecraft since it retired the space shuttle in 2011. But that contract is up at the end of next year. "In April 2018, the program's schedule risk analysis found there was zero percent chance that either contractor would achieve its current proposed certification milestone", the report stated.
"There will not be a requirement for detailed NASA risk assessment", the agency said in a response signed by three officials, including Bill Gerstenmaier, associate administrator for human exploration and operations.
To the final recommendation, NASA is not fully agreed with it, the recommendation is about documenting its tolerance level of risk concerns about the safety of the crew, they argued that it did so years ago even if the existence of other documents on risk requirements "can be confusing".
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SpaceX and Boeing have been vying to be the first to return Americans to space from US soil since 2014, three years after NASA's shuttle program ended.
NASA awarded Boeing and SpaceX fixed-priced contracts - worth $4.2 billion and $2.6 billion - in 2014.
The spacecraft should be certified by 2017, according to the agreement.
Certification of SpaceX's Dragon capsule is not expected until at least January 2020 instead of February 2019.
After multiple test flights, NASA can come back to SpaceX and Boeing and could ask them to make changes or take further steps before a final decision is made about whether the spacecraft is ready to fly astronauts.
This week, Russia's space program upped our standard for "express delivery", shipping 3 tonnes of food, fuel and supplies to the International Space Station (ISS) in just 3 hours, 48 minutes - breaking the record for fastest space cargo mission to orbit.
In this Thursday, July 6, 2017 photo made available by NASA, U.S. Vice President Mike Pence addresses NASA employees, in front of, from left, the SpaceX Dragon, NASA's Orion, and Boeing's Starliner at NASA's Kennedy Space Center in Cape Canaveral, Fla.