The former Miss Universe dropped her layers for the cover of Marie Claire to promote positive and natural body image with unretouched pictures showing a tiny crease on her waist, a slightly dimpled thigh and naturally uneven skin tones.
"It was an absolute surprise to us," Brookes said.
"We control brand Myer, but we do not control brand Jennifer Hawkins. That is up to her manager, Sean Anderson, to do that.
"We were totally unaware of the photographs until we saw them in the paper on Sunday.
"We were disappointed that we were not advised or at least pre-wired (about the shots)."
Myer pays Hawkins well over $1 million a year.
The photo shoot also drew criticism from Aussie radio host Bianca Dye who slammed the magazine for presenting the 26-year-old as a role model for female body image.
Dye, who hosts the breakfast show on i98 FM in Wollongong, objected to the nude pictures, saying it "is just not right" for the magazine to be pushing her as the pin-up for female body confidence.
