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BONITA SPRINGS — The Lee County School District has about 1,000 fewer students enrolled than it did a year ago and is more than 2,000 students below what the state asked it to estimate for the current school year.

This may be the first time the district has lost 1,000 students from the beginning of one school year to the beginning of the next school year, but it is not the first time state enrollment estimates have shortchanged the district.

Coming in below the student estimate for the year, which is produced using a state-mandated formula, will lead to the state taking funding away from the district. As of Thursday, the district was 2,054 students below its estimate of 81,733 students for the year, which would result in the loss of about $10 million in state funding.

And the numbers keep falling, as they have in at least the past two years, Superintendent James Browder said. Between Tuesday and Thursday, the district lost 176 students.

Browder said the district is prepared for the financial hit. The final budget for the year, which is to be presented to the School Board for approval on Tuesday of next week, sets aside $13 million to give back to the state, which equates to about 2,400 students in funding.

“We have — given what we know based on what the economy is doing — added dollars to that portion of the contingency reserve to protect the district,” Browder said. “So, what we’re trying to do is get as much money in that position to protect us as possible. Based on what’s happening right now, I’m certain that we’ll use all that $13 million.”

The district’s head of planning, Mike Smith, said enrollment usually decreases as the year goes on. Last year, the district lost about 2,600 students from the first day of school to the last. The state takes an enrollment count in October and February to determine what funding, if any, it will take back from the district.

“I expect somewhat similar patterns. You never know really what to expect, but the elementary enrollment typically will increase a little bit slightly. The big growth years, we would have roughly 1,300 or 1,400 more (students) by the end of the year. Middle school might drop a bit. High school typically would drop. The end population would be lower than it was at the beginning,” Smith said.

District spokesperson Joe Donzelli said coming in under the state estimate is expected by district officials, due to the inflexibility of the formula being used.

“We fully anticipated coming in under that number,” Donzelli said. “The fact that the state uses enrollment data that is two or four years old. They give us a check for 10 dollars and then a month later say we need $2.47 back, even though, looking at the empirical data, you know the numbers were going to be lower.”