One of the classrooms was also "trashed" including furniture being turned over.
Mackintosh said the burglars had pulled door handles from another classroom and used them "like a hammer" to smash the locks on two storage cupboards.
The iPad covers were found strewn on the school grounds nearby, she said.
Mackintosh said nine of the stolen iPads had been recovered, seven from a bush in Courtney Rd.
Mackintosh said unfortunately due to rain damage the recovered iPads were "stuffed" and seven still missing had been disabled so they were worthless to anyone who had them.
"At $800-odd dollars an iPad, to buy replacements would place extreme pressure on the school's tight budget and financially it's beyond our means," she said.
"These thefts have disadvantaged our students, particularly our special education students who rely on these devices which contained most of their school work."
A police spokesman said police were still investigating the burglary, which involved a group of individuals.
If anyone has further information about the break-in phone Tauranga police on (07) 577 4300 or call Greerton Village School on 07 541 2350