Her representatives did not return calls for comment on Tuesday. Kelly Clarkson and James Taylor, who also performed at the inauguration ceremony, both sang live, their publicists said.
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Whatever Beyonce's choices on Monday, she was not the first artist cause a stir on such occasions.
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Classical musicians Yo-Yo Ma, Itzhak Perlman and two others played along to a pre-recorded tape at Obama's 2009 inauguration because the cold and wind on the Washington Mall raised the potential of broken strings and sharp notes.
Madonna lip-synched her way through her 2012 Super Bowl half-time performance last year, as did the late Whitney Houston in her 1991 Super Bowl rendition of the national anthem. Singing to pre-recorded tracks has become widespread in the pop music industry
The lip-synching question made headlines around the world and "Beyonce" was among the top Facebook conversations on Monday, according to the social networking site.
Fans were divided. "I enjoyed the performance and do not care whether it was lip-synched or not - it was a beautiful rendition, with some originality, of a song we have all heard so many times," wrote LeeAnne24 on the Washington Post comment board.
Twitter user hiphopdancerJen was disappointed. "There's honestly no reason for Beyonce to lip-sync... Especially the national anthem. I may despise most of her music, but she has a voice."
Beyonce is due to take the spotlight again next month - this time at the February 3 Super Bowl half-time show.