According to The Sun, the professional dancer’s feud with the new judge is “undeniable” following their on-air spat last month.
The 41-year-old is believed to have shouted over the bannister at her on Saturday following her low score for Mollie King.
The Saturdays beauty was given a six by Shirley, 57, and it comes after Brendan criticised her remarks about his own partner Charlotte Hawkins.
An insider told the publication that the pair have been at war ever since she took over from Len Goodman – a role he was also tipped for.
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Strictly Come Dancing 2017 in pictures
Mon, November 13, 2017
Strictly Come Dancing 2017: See Charlotte Hawkins, Ruth Langsford, Debbie McGee, Gemma Atkinson and more celebs waltz their way to victory on the BBC dance show.
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Ruth Langsford and Anton Du Beke did the Foxtrot to make The Knife by Bobby Darin
Brendan Cole goes out of his way to ignore her backstage
“Brendan is clearly very bitter about missing out on the role and hasn’t held back on taking out his anger on Shirley,” a source commented.
They continued: “He goes out of his way to ignore her backstage during show breaks and makes her feel very uncomfortable.
“Brendan notoriously falls out with fellow dancers, but this row is on a whole other level. Everyone thinks it’s very childish.”
Strictly Come Dancing 2017: Brendan Cole with partner Charlotte Hawkins
Strictly Come Dancing 2017: Brendan Cole hit back at Shirley Ballas during movie week
The star, who has featured on Strictly since the beginning, has been very open about his disagreement with Shirley and previously slammed her critique.
After she told Good Morning Britain’s Charlotte there was too much “rise and fall” in their Tango, he hit back: “There was no rise and fall in that whatsoever.”
He later added: “She's not my superior, she's a judge on the show and I respect that. I love them all.”
Express.co.uk has contacted a representative for Brendan Cole asking for comment.
Strictly Come Dancing continues Saturday at 6.45pm on BBC One.