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Comptroller Bill Thompson chose the first day of school to stoke long burning disputes over whether the Bloomberg administration has reduced class sizes as much as it promised to.

Thompson accused the Department of Education of redirecting or misspending millions of dollars that he says the department promised to use to reduce class sizes. The audit, which is based on data collected in 2008, states that $48 million of the nearly $180 million set aside for Early Grade Class Size Reduction funding was not used to create new classrooms.

Thompson, a mayoral hopeful, said the DOE has been living in a “childish neverland.”

“To use this money for other things [than class size reduction] is to defeat the purpose,” he said.

Class sizes have risen in the last year despite several programs — either foisted upon the administration or willingly adopted — that aimed to reduce them. The administration has repeatedly portrayed class size as too costly a reform to be realistic. In May, Chancellor Joel Klein warned that average class sizes would increase this year as the size of the teaching force declines.

The dispute centers around whether or not the city committed a set amount of money to be used to reduce class sizes for grades K-3.

In its response, the DOE called Thompson’s report “bizarre,” and said the class size reduction program the comptroller had audited was no longer in existence.

“Accordingly, we reject the Comptroller’s findings, and suggest that in the future he stick to auditing the administration of programs that actually exist,” the statement read.

Though it was repealed in 2007 after a successful lawsuit required the state to give the city’s schools more money, the Early Grade Class Size Reduction program hasn’t entirely disappeared. Under the new funding program, known as Contracts for Excellence, the city agreed to continue “to be committed to reducing class size in early grades (i.e., grades K-3) via the Early Grade Class Size Reduction program.”

The DOE and Thompson diverge in their interpretations of that sentence. According to Thompson, the city agreed to spend the money to reduce class size. But DOE auditor general, Brian Fleischer, whose job it is to oversee regulatory compliance, said that the money is not ear marked and that the city only agreed to ensure that new classrooms that were created in previous years were not lost to budget cuts, not that new ones be created.

“We were free to spend it however we chose,” he said.

Leonie Haimson, executive director of Class Size Matters, said she was asking the state to withhold Contracts for Excellence funds until the city committed to spend money to reduce class sizes.

Thompson’s report also states that the DOE gave $21 million to schools that didn’t have enough space to add classrooms, and that roughly $18 million went to schools that had enough space, but didn’t create new classes.

Fleischer said Thompson’s methodology was flawed because he used enrollment information from January of 2008, after schools’ populations were largely settled, while the DOE had made funding allocations based on projections.