According to British newspaper the Daily Star, Barlow 'hurled his toys out of the pram' following Saturday night's programme.
A source told the publication: 'It was quite a temper tantrum.'
The insider claimed that the 40-year-old had refused to film for Xtra Factor following the two and a half hour opening live show.
The source continued: 'Gary hurled his toys out of the pram and threw a fit. People were shocked it was Gary throwing the strop as he's normally so even-tempered.'
A spokesperson for the Take That singer however dismissed the claims as just a misunderstanding.
His spokesman said: 'There was a chaotic misunderstanding after Gary was told he had been cleared to go for the night and he headed to his dressing room to chill out.
'Producers then realised they still had to do the ITV2 show and staff were dispatched to get Gary back to the studio.
'It all got a bit frantic and disorganised as they tried to explain the mix-up to him and he finally arrived back on the set with 10 seconds to spare.
'Gary doesn't have any plans to quit. He's really enjoying the show, he's having a blast.'