The singer is said to have lip-synched her rendition of 'The Star-Spangled Banner' at yesterday's (January 21) event.
A spokeswoman for the Marine Corp Band told The Times it was "standard procedure" to record a backing track and Beyoncé decided shortly before her performance to use the studio-recorded version rather than sing live.
A representative for the live band told the New York Post: "All music is pre-recorded for the ceremony because there are so many eventualities and conditions that day.
"We performed, live, the band. But we received last-minute word that Beyoncé was going to use the pre-recorded vocal track. Those were the instructions we were given. We don't know what the reason why."
The star's performance was initially well-received by critics, with The Guardian describing it as "poised and confident... it was not definitive, but it was appropriate".
Other performers at the event included James Taylor and Kelly Clarkson, who sang 'My Country 'Tis of Thee'.
Meanwhile, Katy Perry had performed on Sunday alongside Usher and The Wanted at the Kids' Inaugural Concert, organised by First Lady Michelle Obama.
Watch Beyoncé's performance of 'The Star-Spangled Banner' below: