"To allow a child to run where he would have qualified on merit, and then disqualify him is cruel and inhumane," Patterson told Fairfax.
"We haven't broken criminal law here, it's a children's race and we should be encouraging them to participate."
A Lower Hutt School Sports Association spokesman said the rule was there to help protect kids' feet from spiked shoes.
Athletics Wellington director Jo Murray told the Herald she could understand that decision, though she also understood why Henry's mum would be upset.
"You've got a whole truckload of kids at a park, running around between events," she said.
"It's not a rule that we [Athletics Wellington] enforce but I can understand why schools have those rulings."
Murray said the decision, which was made by teachers running the inter-school primary competition on top of their normal duties, would have been about health and safety.
"It's always unfortunate when a kid misses out, but they've obviously just had the rule and made the decision."
Kids were allowed to run barefoot at various other events, including ones hosted by Athletics Wellington and at the Colgate Games, Murray said.