Shouts of "where's Britney?" and even jeers started coming from the audience of 4,300 before she returned to her seat.
The singer, who had missed four more contestants, then reassured fans worried by Twitter rumours: "LOL was just taking a little break people. I am having the best time."
One onlooker said the singer had been unhappy at the crowd reaction to some of her comments — mostly one-word responses such as "adorable" or "amazing".
But X Factor bosses denied Britney, 30, had stormed out or had been upset by the dodgy version of her 2011 hit Hold It Against Me.
Empty chair ... contestant performs as Britney Spears' seat is vacant
And last night there were claims her £9million contract specifically included breaks whenever she wants.
Close pals ... Britney Spears cosies up to fellow judge Simon Cowell
The mum of two appeared nervous in Austin, Texas. Fan Annika Darcy, 33, said: "She was like a rabbit caught in headlights."
'Loving it' ... Britney Spears greets the audience in Austin, Texas
Britney settled down as the seven hours of shooting went on but faced being outshone by fellow new judge Demi Lovato, 19.
Salute ... Britney Spears joins fellow judges Simon Cowell, Demi Lovato and L.A. Reid on panel
The cheeky singer and actress called show guru Simon Cowell, 52, "grandpa" and "old and impatient" and also teased the fourth judge, record exec LA Reid, 55.
'Having the BEST time' ... Britney Spears at X Factor USA auditions in Austin, Texas
Cowell jokingly threatened to make Demi sit in the "naughty chair".
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