The professional dancer became very defensive when the head judge critiqued his dances with celebrity partner Charlotte Hawkins earlier this series.
Now, Shirley has revealed that she was taken aback by his reaction despite knowing the dancer for a long time.
“I know what Brendan’s like,” she told TV Times. “I taught him for a long time and we were very close back then.
“I was quite surprised he said what he said, but I actually adore him, he’s a very educated man.”
However, Shirley went on to add: “I can’t control what comes out of his mouth, he has to take responsibility for what he chooses to say.
“I don’t choose to be that negative person and I definitely never have to pull somebody down to put myself up.”
The 57-year-old, who took over from Len Goodman, also hinted that this may be her first and last series as she opened up about the hurtful comments she sees from fans on social media.
When asked what the most surprising thing about Strictly was, she told the publication: “The trolls on social media, the people that sit behind a computer and call me the most ghastly names that even your worst enemy wouldn’t make up
“[…] I love constructive criticism, but this is cyber bulling from cowards hiding and it’s overwhelming.
“They tell me not to read it, but of course I want to. I hope that beyond social media, families in their living rooms are enjoying the job that I’m doing.”
Read the full interview in this week’s issue of TV Times, which is out now.
Strictly Come Dancing airs Saturday on BBC One at 6.50pm.