WASHINGTON — By the first week of January, when U.S. Air Force Secretary Deborah Lee James called SpaceX founder Elon Musk, the relationship between their two camps was already knotted and tense.

The Air Force and SpaceX were still tangled in a lawsuit over the service’s sole-source contract to the company’s archrival, United Launch Alliance, for a large batch of rockets. Meanwhile, the Air Force still had yet to certify SpaceX’s Falcon 9 rocket to carry national security satellites despite pledging to do so by the end of 2014.

Now, James had bad news. She told Musk that it would take another six months to certify the Falcon 9, effectively taking SpaceX out of the running for a U.S. National Reconnaissance Office launch contract worth more than $100 million.

SpaceX executives — and even some Air Force officials — were surprised. “The company thought (they) were there,” one industry official said.

A report released March 27 details why certification has taken so long and how the process strained the relationship between the Air Force and the upstart rocket company.

In short: SpaceX believed its track record dating back to 2013 should have given the Air Force confidence in its rocket and was slow to embrace the service’s need for large volumes of data, the report said. The Air Force, meanwhile, viewed the certification process as a kind of design review and pushed SpaceX to make dozens of changes to its Falcon 9 rocket, processes and organizational structure.

The review panel was headed by retired Gen. Larry Welch, a former Air Force chief of staff, Lt. Gen. Ellen Pawlikowski, the service’s top uniformed officer for acquisition, and SpaceX President and Chief Operating Officer Gwynne Shotwell.

“There is a large gap between the perceptions of the partners,” the report said. “There is also a lack of common understanding of some basic objectives and definitions embodied” in the Air Force-SpaceX agreement on the certification requirements, the report said.

Air Force and SpaceX officials have declined to release even a redacted version of the June 2013 Cooperative Research and Development Agreement.

Air Force officials have said that as part of the agreement, staff at the service’s Space and Missile Systems Center (SMC), which buys military space systems, would review data from three Falcon 9 launches and study the vehicle’s flight history, design, reliability, process maturity, safety systems, manufacturing and operations, systems engineering, risk management, and launch facilities. Hawthorne, California-based SpaceX successfully launched those missions in late 2013 and early 2014.

But the precise meaning of certification was poorly understood, the report said.

“It needs to be clear that the Certifying Official is not certifying readiness to launch,” the report read. “Instead, the certification should be a declaration of confidence in the New Entrant’s ability to satisfactorily meet all the requirements to successfully deliver to orbit on schedule with the defined level of risk.”

The report also details a level of misunderstanding, if not mistrust, between the two sides.

SpaceX was slow to understand the Air Force’s certification data requirements and often felt the service was being prescriptive, the report said.

“The SpaceX view is that the Air Force should have confidence in SpaceX capabilities based on its track record of performance,” the report said.

SpaceX’s perception that it was being over scrutinized was evident during a March 17 hearing of the House Armed Services Committee.“It bears noting that the New Entrant Certification requirements that SpaceX must live up to vastly exceed the requirements that the Atlas 5 and Delta 4 launch vehicles had to meet in 1998, prior to their ability to compete for” military launch contracts, Shotwell said in written testimony. The Atlas 5 and Delta 4 are the two main rockets operated by ULA.

The Air Force, the report said, was slow to embrace SpaceX’s innovations. The service also sought to dictate “conditions to SpaceX in detail without a productive structure or process to resolve issues as they occur,” the report said.

Ultimately, SpaceX had little recourse but to begin giving the Air Force what it wanted, the report said. “This can be the worst of all worlds, pressing the Falcon 9 commercially oriented approach into a comfortable government mold that eliminates or significantly reduces the expected benefits to the government of the commercial approach,” the report said.

Approximately 400 certification items were still outstanding when work on the report concluded. The report suggested that some of these issues could wait until after the Falcon 9 is certified, which would require a departure from Air Force practices.

“It is neither possible nor should it be necessary to close all the issues by the certification date as currently required by language in the agreement,” the report said.

Among the major remaining certification issues identified in the report: SpaceX integrates satellites to its rockets horizontally, but the Air Force prefers vertical integration; GPS-based launch vehicle tracking; information assurance; and secure flight termination.

James said in a March 23 press release that the two parties are focusing on second-stage-engine and fairing qualification and contamination control. “I look forward to continuing to work with SpaceX on this final portion of our certification effort,” James said in a prepared statement.

Despite the misunderstandings, certification appears to be on track, sources say, and SpaceX has seemingly offered an olive branch to the Air Force. During the hearing, Shotwell said SpaceX and service were working “shoulder to shoulder” on certification.

A second report on how the Air Force can improve its certification process is expected later this year, said Capt. Chris Hoyler, an Air Force spokesman. ULA is expected to be part of those conversations as it will need to certify the new vehicle the company says it is developing to replace the Atlas 5 and Delta 4.