The source told the Daily News the rare test results were part of the "highly unusual circumstances" a spokesman for Braun had previously referred to in refuting the report of Braun's positive test.
The Milwaukee Brewers outfielder and National League MVP tested positive for a high level of testosterone deemed synthetic and not natural, according to an ESPN report, and he faces a possible 50-game suspension.
Braun and his agent have vehemently denied Braun knowingly took an illegal substance, with Braun telling USA Today, of the positive result, "It's BS."
Braun's spokesman, Matthew Hiltzick, also issued a more formal statement supporting Braun's innocence.
"There are highly unusual circumstances surrounding this case which will support Ryan's complete innocence and demonstrate there was absolutely no intentional violation of the program," the statement read. "... we are confident he will ultimately be exonerated."
The test results were "insanely high, the highest ever for anyone who has ever taken a test, twice the level of the highest test ever taken," the source told the paper.
Braun plans to appeal any suspension from the positive test, which came as a shocker to a sport trying to move on from the stains of the steroid era and had just set up an agreement to begin Human Growth Hormone testing in the last Collective Bargaining Agreement.
He will not have to worry about the status of his MVP award as Baseball Writers Association of America secretary-treasurer Jack O'Connell told the Los Angeles Times the organization, whose members vote on the award, will not strip Braun of it.
"The voters used the information they had at the time of the election," O'Connell said, also saying there were similar questions when admitted steroid user Ken Caminiti and PED-user Alex Rodriguez were named MVPs. "I don't see how we can change that."
The positive test reportedly came during the playoffs before the St. Louis Cardinals beat Braun and the Brewers in the National League Championship Series.
The test results were sent to the World Anti-Doping Agency lab in Montreal for another test, thought to be more reliable, the source told the Daily News. The levels were reportedly revealed in that test to be synthetic.
While the high levels were considered unusual, the source told the Daily News the appeal will be based not on those levels because "it's not something (Braun) knew or should have known about," but that there were other factors.
There were issues with the chain of custody with the test, the source told the Daily News.
Braun is aware that simple lack of knowledge or intention is not a viable defense, but sources told the News there was still an adequate defense to be prepared because "this is not like the other cases," one told the paper.
No player has yet successfully appealed a positive test result in 13 tries, but Braun has been eager for his attempt to set a precedent, telling the Milwaukee Journal-Sentinel, "I can't wait to get that opportunity. This is all BS. I am completely innocent."