LAST week, the New York State Legislature struck a deal ensuring that charter schools in New York City would have access to space, either in already crowded public school buildings or in rented spaces largely paid for by the city. Over the next few years, charters are expected to serve an increasing proportion of city students — perhaps as much as 10 percent. Which brings up the question: Is there a point at which fostering charter schools undermines traditional public schools and the children they serve?

The experience of Harlem, where nearly a quarter of students are enrolled in charter schools, suggests that the answer is yes. High-quality charters can be very effective at improving test scores and graduation rates. However, they often serve fewer poorer students and children with special needs.

In Harlem, there is a marked disparity between the special-needs populations in charter and traditional public schools, according to the city education department’s annual progress reports. In East Harlem, data for the 2012-13 school year shows that most of the public open-enrollment elementary and middle schools have double, and several have triple, the proportion of special-needs kids of nearby charter schools. At most of these public schools, at least a quarter of students have Individualized Education Programs, or I.E.P.s, which are required for children who receive special-education services.

Students with I.E.P.s also tend to leave New York City charter schools at higher rates than their general-education classmates, according to a 2014 study by the city’s Independent Budget Office. Among special-needs students enrolled in charter schools in kindergarten in 2008, 27 percent had transferred to a traditional public school by third grade; the corresponding rate for general-education students was 17 percent.

Some students with I.E.P.s find charters, which often foster a no-excuses culture, a poor fit, and leave voluntarily. But sometimes there’s pressure: Administrators may advise parents that the school can’t support a child’s disability, or punish kids for even the slightest disciplinary infractions. However it happens, it leads to rising special-needs populations at nearby public schools.

Chrystina Russell, the founding principal of Global Technology Preparatory, a Harlem middle school, says charter-school “refugees” often showed up at her school after Oct. 31, when the Department of Education makes key funding decisions for traditional public schools based on head counts. This means that it can be difficult for the schools to hire additional teachers or support personnel when new students show up (though some funding is updated for special-education students who transfer by Dec. 31).

Global Tech had no post-October transfers this year, but had as many as eight two years ago. Nearby Isaac Newton Middle School for Math and Science has had about a dozen so far this year.

Global Tech, where more than one-third of the students have I.E.P.s, does impressive work despite the challenges. If special-education kids — most of whom are black and Hispanic boys — are segregated when they get to high school, they are unlikely to graduate. So Global Tech is committed to mainstreaming them in general-education classes by the eighth grade. Instead of suspending disruptive students, the school takes away extracurricular sports privileges and holds lunchtime detentions and meetings with parents. Some of its special-needs students have been accepted to the best public high schools in the city.

As charter schools demand an ever larger share of public resources, they insist that they teach a full spectrum of public-school students. But there is abundant evidence to the contrary. Charter schools are free of most regulations governing traditional public schools, including some admissions rules for special-needs students. The latest battleground is over financial audits — a State Supreme Court justice in Manhattan ruled last month that city charter schools do not have to submit their books to state auditing, even as Albany drafted legislation requiring audits by the city comptroller.

If charter schools are allowed to push out existing public schools, they should, at the very least, be subject to the same accountability measures for enrollment, attrition and disciplinary procedures, to ensure that the neediest students are being treated fairly.

It’s understandable that kids and parents feel passionately about their schools, whether charter or public. But it is important to recognize the differences between the two and the roles they play for what are often very different student populations. Some charter school initiatives, like longer school days and student-reward systems to foster good behavior, have been adopted by traditional public schools. But charters have a lot to learn from these schools, too, especially when it comes to educating special-needs students.

We should not allow policy makers to enshrine a two-tier system in which the neediest children are left behind.