Addressing a common criticism of New York City charter schools, a study released on Thursday said that in general their students were not, in fact, more likely to transfer out than their counterparts in traditional public schools.

But the study, conducted by the city’s Independent Budget Office, concluded that special education students left charter schools far more often.

The findings shed light on a sector that mushroomed in the 12 years of the Bloomberg administration, with 150 charters now operating in the city. Though they serve just 5 percent of pupils, charter schools garner an outsize portion of debate because they are financed by taxpayers but privately managed, they often take space in public schools, and their teachers are usually not unionized.

Mayor Bill de Blasio has pledged to charge rent to charter schools with significant financial resources, such as those backed by philanthropists. Charter operators who have received free space for years are concerned.