It was standard procedure to record backing tracks for inauguration performances, where cold weather is often a factor, she said.
"We pre-recorded all music as a matter of course and have done since time immemorial," she said. "This is our 54th inauguration... There is no question of there not being any music - it's not because the performer cannot do it."
A representative for Beyonce did not immediately respond to requests for comment.
Kelly Clarkson's representative said she sang live to perform My Country, 'Tis of Thee.
The use of a recording is typical in big events. In 2009, cellist Yo-Yo Ma was questioned about "hand-synching" for Obama's first inauguration. Ma said instruments weren't functioning properly in 19-degree weather.
It wasn't the only controversial performance of the day.
Rapper Lupe Fiasco was removed from the stage at an inauguration party concert after singing a song that included anti-Obama lyrics.
Organisers insisted he was only asked to leave the stage because his performance "wasn't up to scratch".
- Herald Online and AP