The U.S. Air Force and SpaceX are modifying the Cooperative Research and Development Agreement (CRDA) signed two years ago to outline what has become the contentious process to certify the Falcon 9 v1.1 rocket for use in launching national security payloads.

The changes are needed to refocus the certification process on establishing top-level trust and confidence that the company can deliver a launch as planned. The current CRDA was “probably too focused on the government side on conducting detailed design reviews and instructing design changes … rather than focusing on the high-level question of do we trust this new entrant,” Air Force Secretary Deborah Lee James told Aviation Week during a March 25 interview.

SpaceX chose its path to certification and the CRDA was signed by both parties in June 2013. “Even though the certification process is governed by a CRDA – it is all written down – and you would think that would help people mutually understand what is expected, that, in fact, was not always the case,” James said. SpaceX’s culture of innovation and the Air Force’s culture — focused on “history and a lot of experience” — clashed.

The CRDA has not been publicly released, but both parties have said it required SpaceX to conduct three successful Falcon 9 launches, two of which were to be consecutive. These missions were completed by January 2014.

Additionally, they say the company was required to provide data for review on its designs and processes as well as engineering analysis, though detail on this element has been scant. This is the portion that has taken the most time for SpaceX.

The options for SpaceX in setting up the CRDA were as follows:  three launches with 3-4 years worth of engineering analysis, six launches with a reduced data requirement, or 14 launches, which would have triggered an “automatic” certification, according to industry officials. “We would probably already have met the requirement” for the six launches and reduced data, one industry official says. To date, SpaceX has conducted 12 Falcon 9 v1.1 flights.

James says detailed review is “quite appropriate as you get close to the final launch decision, but not appropriate this early on” in the process. “This certification moving  forward should [focus more on] ‘Do we have confidence in their process, their procedures [and] what they’ve demonstrated to us that they can get from there to there on time.’”

James announced the review was being done in January; Air Force Gen. (ret.) Larry Welch, former chief of staff, led the independent review team on the certification process. James’ comments are based on the findings of the first phase, which was to specifically look at SpaceX’s experience with Falcon 9. SpaceX founder and Chief Technology Officer Elon Musk accused the Air Force of dragging the process out. He claimed that at least one former Air Force official was too cozy with industry rivals after accepting a post-service position; he said this was behind an anti-SpaceX bent in the service. During a March 17 hearing, Gwynne Shotwell, president and chief operating officer of SpaceX, said this accusation was not “borne out.” Still, however, James was under pressure to ensure the process is fair moving forward.

Welch is proceeding with the second phase of the review, which will examine how to conduct certifications in the future.

James says in the future one thing to consider would be how to accept a company’s planning for its certification path. “Part of confidence is even if you can’t do every single thing right now, do you have a believable plan to get there from here,” she says.

Based on certification rules, SpaceX is allowed to compete with the United Launch Alliance (ULA) monopoly for work but cannot win a launch until it is certified. SpaceX dropped a lawsuit against the Air Force in January; the company claimed a 36-rocket core deal with ULA unfairly cut its Falcon 9 out of the market. The parties have not said what the agreement was to drop the lawsuit, but the Air Force is planning to compete nine launches through the end of fiscal 2017.

Once Falcon 9 is certified, Shotwell says the company plans to request certification for the Falcon Heavy, which company officials hope to fly this year. It could compete to lift heavier payloads now handled by ULA’s high-end Atlas V, and even some Delta IV payloads. Likewise, a forthcoming launch system that will likely replace the Atlas V will undergo certification.