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Anyone who stayed until the bitter end of a three-hour meeting last night about kindergarten waitlists in Manhattan got a surprise: an uncharacteristic apology from a top DOE official.

Hundreds of parents turned out for a meeting of the parent council for District 2 to vent about having been shut out, at least for now, of their neighborhood schools. Last week, Manhattan parents protested at City Hall after 273 children were put on waiting lists at many elementary schools.

Deputy Chancellor Kathleen Grimm arrived late to the meeting after spending her afternoon dealing with the swine flu outbreak in Queens. She sat quietly in the audience and listened to a tense back and forth between school officials and angry parents. The auditorium had mostly emptied and council members were preparing to adjourn when Grimm approached the microphone to make a surprise statement, which I captured on video above. Here’s a key part of what she said:

I also want to say something that I thought I heard people from the DOE say tonight, but just in case you didn’t, I want to say, I’m sorry. We’re sorry. We have stumbled on some of this planning.

The two officials leading the meeting told parents during the meeting that most schools should be able to eliminate their wait lists by the middle of June, after families find out where they’ve been offered seats in gifted and talented programs. John White, who heads the Department of Education’s efforts to manage school space, said that more children in each area qualified for gifted admissions than there are children on the waiting list.

Simply qualifying for gifted programs does not assure a child a seat in the programs, which have far fewer seats than there are eligible children. But White said that he is confident that the wait list numbers give an inflated sense of how many children will actually not find spots, noting that if the pace of enrollment growth suggested by the wait lists is real, it would be a substantial departure from past years.

If every single child on the waiting lists in Greenwich Village and on the Upper East Side actually attended the school they are listed for next year, kindergarten enrollment in each neighborhood would be a third higher than last fall, he said. In recent years, those neighborhoods have seen annual growth in kindergarten enrollment of 1 to 7 percent. (According to discussions on the Urban Baby Web site, many families haven’t yet made up their minds about whether to enroll in public or private school for the fall.)

Parents last night received White’s reassurances that children would find spots and that the DOE is working on a plan to prevent the problem from recurring with strong skepticism. Elizabeth Rose, the PTA president at PS 183 on the Upper East Side, where there are 31 zoned children on the wait list, said, “We have no confidence that gifted and talented will clear that number.” Other parents asked how the department plans to accommodate families who move into a school’s zone over the summer. And others hammered away at what they said is the core issue, the city’s failure to meet projected enrollment increases with new school buildings.

“Are you all happy with what you’ve heard tonight?” asked parent council member Michael Markowitz at one point midway through the meeting. “No!” audience members shouted in response.