Parents and carers at Aboyne Primary School in Aberdeenshire complained after they were sent a link from Tempest Photography offering an alternative image.
Three children were removed. One was Erin Pinnell, nine, whose mother Natalie said she was "devastated" when she received the email.
She described the decision taken by the company as "inhumane" and said her child had been "erased from history". Natalie, 38, said: "You can't erase them because they're inconvenient. It's just not OK.
"It's devastating to have your child be erased from a photo or give parents a choice whether she should or should not be included.
"She is the most beautiful human being. Who could do this?
"I'm grateful that she's not aware of it because the damage that would do to her self-esteem would be devastating. But I'm having to tell my other daughter what's happening to her sister." The mum of two said
Aboyne Primary School had also apologised but was keen to emphasise: "It's not the school's fault."
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