The error also overpaid some schools $6 million, The Arizona Republic reported Sunday.
The mistake was discovered during a meeting of school business officials.
The money, raised from a 0.6 percent sales taxes approved by voters in 2000, goes into an account dedicated to teachers' salaries and providing classroom instructional support.
The error was caused, officials said, by calculating payments based on current school enrollment figures rather than prior-year enrollment.
State Department of Education officials said underpayments would be distributed to school districts and charter schools in a lump sun in March. Overpayments will be recovered by reducing allotments to the schools over the next 17 months.
The largest single underpayment was $3.3 million to Mesa Public Schools, officials said. The largest single overpayment was $324,000 to a charter school.