The employees are being notified this week. It's a very complicated accounting problem and the solution isn't an easy one either.
The notice went out to about 3,700 HISD employees and affects 12-month employees, which means most teachers are not affected.
The district says the problem dates back to the year 2000, when they converted to a new payroll system. As employees left or retired, they were being told they owed HISD.
"It's just not a good way to do business, so we're trying to clean all that up," HISD Spokesman Jason Spencer said.
Spencer admits the district didn't do a good job early on of informing employees and says they have an obligation to the taxpayers.
"We're attempting to reconcile that. We're going to all of our employees, we're letting them know how many days in advance they were paid for time that they did not work," Spencer said.
Employees will be given three repayment options: They may give back earned time off; have regular paycheck deductions for up to two years; or make a one-time payment back to the district.
Gayle Fallon with the Houston Federation of Teachers raises several questions about the memo, including the statute of limitations.
"You don't go back and tell an employee that you are going to pay us something from eight years ago. We're going to suggest to our members, tell them no, make them sue you," Fallon said.
While teachers in the union are not affected, she's concerned about the employees at the bottom of the pay scale who are.
"I'm very worried about the clerks and the secretaries. It won't sound like a lot of money to the public, it is a lot of money, every dollar counts," Fallon said.
This could be as much as four weeks pay for some employees. The district says once this is corrected, it will not happen again.