Some students even reported their noses being changed and monobrows removed. 

In a prepared statement, principal Graeme Holmes said the school took the "wrong approach" in removing piercings from the school photos.

He said original portrait photos would be offered at no cost to families.

However, many students said it was too late. 

Jacki Lipplegoes, who had her piercing removed in a photo, said she was disappointed the photo did not "show the real her". 

"We paid for a photo to show how we looked in 2015, but this isn't how we look," she said.

"Our identities have been changed and it doesn't make you feel too good at all."

A mother of a student, who wished to remain anonymous, said her daughter and fellow students were devastated when seeing their photos. 

"As parents, we know that they're proud of those differences and it means a lot to them," she said.

"They're just trying to find who they are but this has been stripped from them. It's just not right."

Michelle Roberts, whose son attends the school, said students' freckles had been removed.

She said image and identity were so important for adolescents and should be nourished, not rejected. 

"Often (their appearance) is all they feel they have any control, say and self expression over," she said.

"Schools need to get over the hair-dye and piercing thing. Is it really so bad when an adolescent wants to express themselves in the way they look?"

But Mr Holmes said the changes had been made due to school policy. 

He made no mention of the school removing freckles, acne or blemishes. 

"While students are allowed to have facial piercings, those piercings must only be studs, and cannot include rings, sleepers or hoops due to safety reasons," he said. 

"Next year, we will ensure that students have plenty of notice that they will only be able to participate in school photos if they meet our uniform policy."