The education provider offers holiday and after-school programmes for primary school-aged students.
Police said emergency services were called following a report of a vehicle crashing into a building on Anzac Rd in Browns Bay.
A police spokesperson said the driver was assisting with inquiries into the circumstances of the crash.
St John said staff treated two patients at the scene before transporting them to Starship Hospital. One had serious injuries and the other had moderate injuries.
The staff member said the mother was more injured than the girls, and that the girls were okay.
A witness who saw the incident unfold said the vehicle had smashed several metres through a glass conservatory where children were waiting for a class.
"Unfortunately [she's] knocked over a couple of kids at the same time."
The noise of the car smashing through glass and aluminium joinery meant he initially thought scaffolding had fallen over, he said.