Kent Police have written to every school in Swale to warn that rising scrap metal prices has contributed to a rise in lead roofing thefts.
Officers said Holywell Primary School, Hartlip Endowed Primary School and Newington Primary School had been targeted in the past month.
The total repair bill for the three schools is estimated to be £6,000.
Adrian Fromm, a crime reduction officer with Kent Police, advised schools to use anti-climb paint to deter thieves.
"Unfortunately the effects of metal thefts can be far-reaching," he said.
"The theft of any lead can result in rainwater leaking through the roof into the fabric of the building, which can cause untold damage to schools."