The veto stirred outrage among Republicans.
"His stance defies logic and demonstrates his blind hatred for public school choice," said State Sen. Jeffrey Piccola (R., Dauphin).
Charter schools that own their own buildings are already exempt from property taxes. The provision in question would have extended that exemption to any nonprofit landlord that rented property to a charter school.
Some foundations that serve as landlords already get such a tax break, but some do not. The office of Sen. Majority Leader Dominic Pileggi (R., Delaware), who sponsored the bill, said it would affect just three schools: the Collegium and Avon Grove charter schools in Chester County and the School Lane Charter School in Bucks County.
Rendell contended the provision was unconstitutional because it didn't extend the exemption to landlords who rent to other nonprofit tenants, like senior centers or religious groups.
"That, in and of itself, violates the Uniformity Clause of the state Constitution, which requires uniformity of taxation,"said Rendell.
Piccola called the veto a "final, mean-spirited act" of the outgoing governor.
"This bill represents two years of bipartisan efforts by both Chambers to make our schools safer and better," Piccola said in a statement.
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Staff writer Amy Worden contributed to this article.