The official also told CNN that Beyonce herself has decided on Sunday not to perform live, as she had arrived too late to have proper rehearsal time with the US Marine Band.
On Tuesday, the US Marine Corps confirmed that, instead of its band playing live to accompany Beyonce, a pre-recorded version of the anthem was used.
But it added that, as far as the Grammy-winning chart-topper's vocal performance was concerned, it was not in a position to say whether or not she sang live.
In Britain, a veteran audio engineer said it looked to him, after examining online videos, that Beyonce did indeed sing -- but it was uncertain whether her singing was relayed over the loudspeakers to the sprawling audience.
"There's no question at all in my mind that she was singing as she stood on the stage and that it (her voice) was going into a microphone that was live," Ian Shepherd told AFP by telephone.
"The question is, who got to hear what came through that mic? Did it go out to the crowd?"
Soul legend Aretha Franklin and younger singing stars Alicia Keys, Jennifer Lopez and LeAnn Rimes sprung to Beyonce's defense, with Franklin saying it made sense to go with a backing track given the near-freezing temperatures.
"She did a beautiful job with the pre-record," Franklin, 70, who sang at Obama's first inauguration four years ago, told ABC News. "Next time I'll probably do the same."
Beyonce herself was last seen dining out in New Orleans late Monday after attending the inauguration with her hip-hop husband Jay-Z.
Beyonce rarely uses Twitter, but her Tumblr account features many photos from Monday as well as a video captioned: "Beyonce sings the national anthem ... at the 2013 presidential inauguration ceremony."
Shepherd, who has worked with musical acts as diverse as Culture Club, Tricky and the Berlin Philharmonic, examined at least three different online videos of Beyonce's performance.
On his website, Mastering-Media.co.uk, he said it was understandable that, on a cold day, Beyonce would favor a pre-recorded track over singing with the Marine Band, which by that point had been out in the open air for hours.
"Any singer would find it seriously difficult to put on a great performance to a band that was struggling to play in tune," he wrote.
"And for something this high-profile it's understandable that you'd want the best chance to get it right," he said.
Beyonce, who sang "The Star-Spangled Banner" at the Super Bowl last year, returns to the American football classic February 3 for its half-time show. She also has a documentary about her life airing on HBO television on February 16.
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