Nearly 2,500 children are on wait lists for their zoned kindergarten programs this year, according to data released by the Department of Education today.

Their parents will have to wait until the end of June to find out where they will be offered a kindergarten seat instead. Last year, families received alternate spots in mid-April, but the wait lists tend fluctuate so much that the department decided to delay making assignments that would likely have to change families will away, enroll their children in private or parochial schools, or win lotteries for charter school admission.

About 600 more students than last year have applied for kindergarten. But there are about 600 fewer children on waiting lists than last year at this time.

The wait list numbers reflect an annual rite of spring as parents register at their nearby elementary schools but land on wait lists because there are more zoned applicants than there are kindergarten spots.

The phenomenon is highly stressful for families who are told they cannot be accommodated. But it is not widespread: Of the total number of families that have applied for kindergarten so far this year, just 4 percent were placed on wait lists.

There are wait lists at 125 schools, the same number as last year at this time. At half of those schools, the wait lists are shorter than 10 students, making it likely that everyone who has tried to register at the school would be accommodated by September.

Three schools — two in Brooklyn and one in Queens — have more than 100 students on their wait lists. The schools are P.S. 169 and P.S. 94 in District 15 and P.S. 304 in District 24. P.S. 41, located in Greenwich Village, is the most overenrolled Manhattan school with 55 children on its wait list.

DOE officials emphasized that between now and the end of May the wait list numbers would likely fluctuate and that most families would wind up with kindergarten spots close to home. In 2010, about 1,000 kindergarteners could not be accommodated in their zoned schools.

“We know that this can be an anxious time for parents, but we can expect these lists to shrink and disappear by the first day of school in September, as they have every year,” said Frank Thomas, a department spokesman, in a statement.

The wait lists do not reflect another phenomenon that stems from excess kindergarten enrollment: The reduction of pre-kindergarten spots. Some schools have shrunk or eliminated their pre-K programs in order to accommodate increasing demand for kindergarten spots.