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New York City’s process for assigning students to schools still sets some of the schools up to fail, State Education Commission John King charged today.

“I continue to have concerns about enrollment,” King said. “I worry about the over-concentration of high-needs students in particular buildings without adequate supports to ensure success.”

King made the comments to reporters during a break in a meeting of Gov. Andrew Cuomo’s state education reform commission, which met this morning in the Bronx.

City officials have acknowledged King’s concerns when petitioning the state for aid, but they have never conceded that high concentrations of needy students could hurt schools. Today, the Department of Education official in charge of enrollment said recent changes to the way some students are assigned to schools, made quietly last summer, were meant to increase choices for families, not respond to King’s concerns or help struggling schools.

King’s concerns reflect longstanding criticism about the Bloomberg administration’s school choice policies. For years, critics have charged that the department overloads some schools with needy students, making it hard for them to show progress or even sustain their past performance. An internal department report completed in 2008 and obtained by GothamSchools last year concluded that a high school’s size and concentration of low-achieving and overage students strongly predicts its graduation rate.

At many schools the city has closed, performance had fallen as populations of English language learners, poor students, low-scoring students, students with disabilities, and overage students increased, often after other nearby schools were shuttered.

But department officials say some schools have improved and even thrived despite having challenging student populations. The deputy chancellor in charge of enrollment, Marc Sternberg, told reporters today that some schools had gotten “outrageously better results” with similar students.

The argument is valid but not sufficient, King said.

“I agree with the city’s perspective that indeed there are schools that have very high concentrations of high-needs kids that are excelling,” he said. “The question is how do we ensure where there are concentrations of [those students], there are adequate supports. If not, how do we think about the enrollment system to make sure that students have access to schools that will provide the support that they need?”

King first expressed the concerns a year ago when awarding the city aid for schools it was closing and reopening. He said he wanted ”to ensure that schools receiving students who would otherwise have attended a phased out school are not negatively impacted as a result of their now enrolling an increased number of high-needs students,” a scenario that he noted had played out before in the city.

Today, he said his renewed criticism would not come as a surprise to city officials.

“Chancellor [Merryl] Tisch and I have raised concerns about this repeatedly with the city,” King said. “We think this issue of how you manage enrollment is critical to effectively managing a system of 1,700 schools, and I think ultimately the mayor, the chancellor, and the deputy chancellor, [Shael Polakow-Suransky] came to agree with that view.”

Last summer, the department quietly embarked on a pilot program to distribute students who enroll in the school system during the school year and summer over a wider swath of schools. Those students, known as “over-the-counters,” include immigrants and teens who have been incarcerated. The city gets about 20,000 high-school-aged over-the-counters each year, and last year, about 800 of them went to 54 high schools that had not been slated to accept midyear arrivals, according to a memo the city sent to the State Education Department last month.

The memo was aimed at smoothing the city’s chances of receiving federal School Improvement Grants for 24 struggling schools. King was responsible for distributing the aid, and he had pushed the city to explain how it make sure the school would enroll students whose needs mirrored the district’s as a whole.

In the memo, the city appeared to acknowledge that King’s concerns about student distribution had merit.

“We acknowledge that there is still more work to do,” the memo said. “Over the past 18 months, NYC has been working with the New York State Education Department to address its concerns about situations where our choice-based system may be leading to an over-concentration of students” with high needs.

But Sternberg said today that the recent changes were aimed at offering more choices to over-the-counter students and their families, not distributing high-need students more equitably.

“I think we acknowledge that the state has concerns … and we want to be sensitive to those concerns,” he said. “Our position is we want to provide families as many options as possible.”

He added, “I have a lot of respect for John King. If this is something that John is concerned about we want to be sensitive to that concern.”

King cited the city’s letter when he conditionally approved the federal grants last month, saying that the department had pledged to “aggressively manage” over-the-counter enrollment in the schools.

Today, he said those promises would have to be reassessed now that the city’s school “turnaround” plans, which would have received the funds, have collapsed.

“There are some things that the New York City DOE agreed to do based on their SIG application, but now all of that obviously has to be reviewed, revised, and revisited in light of the arbitrator’s and court’s decision,” King said. “But we’ll continue to have that conversation with the city because we want to be sure that we don’t have those over-concentration of high-needs kids.”

UFT President Michael Mulgrew said today that the changes to the over-the-counter policy were long overdue — and not extensive enough to repair the damage wrought by the city’s school choice policies. “Those are band-aids on this problem,” he said. “The only reason they are even slightly adjusting this is that John King is asking them to.”

King signaled that he had been discussing the issue with not only Sternberg, but with Chancellor Dennis Walcott and Polakow-Suransky as well. ”They have been open to discussions with us about how they might tweak enrollment policies to ensure that schools have the right supports in place,” King said.

Those changes are sorely needed, said Robert Hughes, the president of New Visions, a nonprofit that works in or operates dozens of city schools, including some that were eligible for School Improvement Grants.

“I think we do need to figure out a mechanism to ensure that that need is more equitably distributed,” Hughes said. “It’s pretty clear that concentration of student need, and a school’s ability to personalize instruction, has an impact on whether or not a school is successful.”