The singer, who's sold 81 million singles worldwide, was appointed to a judge a nationwide video competition in Australia by the telecommunications company Telstra.
Perry chose to award the Loreto Mandeville Hall school in Melbourne, which charges pupils $22,000 (£14,000) a year to attend, according to The Daily Mail newspaper.
Lisa Murphy, who leads a dance program for children and young people with special needs, told The Daily Mail: "It's a waste of money.
"Nothing against Loreto, and I'm not saying we should have won as we don't have much money to produce a great quality video, but there are other establishments for special children that could have done with the $10,000 more.
"We are wanting to develop a program to take into special schools. Most don't have a performing arts program at all and children with special needs have a strong creative flair and learn creatively, not through traditional methods."
Other schools in Australia have criticised Katy Perry's decision.
Katy Perry was raised in the church and began her musical career as a Gospel artist, attending a private Christian school in California.
She visited Loreto Mandeville Hall school personally to tell them they'd won the competition.
According to The Daily Mail, she said: "I picked you guys out of 300 different submissions from all over Australia, there are four girls that we should all thank because they made the most adorable, sweet, innocent, full-of-life, full-of-joy video - and I picked that one."
Telstra spokesman Fady Taouk told the Daily Mail: "Every school in Australia was given the same equal opportunity to enter and win the competition, with entries judged on their creativity."