Reversing its earlier findings, the Independent Budget Office released numbers Thursday showing that charter schools have done a slightly better job retaining young students with disabilities than neighboring district schools.

The report updates IBO data released last year showing that charter schools were losing 80 percent of kindergarten students with special needs within three years. The new numbers show that 53 percent of charter-school students with a disability who started kindergarten in 2008 stayed at their school until fourth grade, while 49 percent of students with a disability did at a sampling of nearby district schools.

The report is likely to reignite debates over how well the city’s charter schools serve high-needs students. The charter advocacy group Families for Excellent Schools seized on the numbers on Thursday to criticize Chancellor Carmen Fariña, who has called on charter schools to serve their “fair share” of high-needs students and said she believed some charter schools were pushing students out before the state tests.

“I certainly think this report should inform the debate, and I hope it would stop some people from claiming that charter schools experience higher attrition than district schools when this shows exactly the opposite,” New York City Charter School Center CEO James Merriman said.

The IBO’s about-face on special-education retention numbers is the result of its use of a broader definition for students with disabilities. Last year, the IBO looked only at students receiving full-time special education services, leaving out a significant portion of students that the city classifies as having a disability. (IBO officials acknowledged that gap to Chalkbeat last February, but did not release updated numbers then.)

The IBO’s new figures show that charter schools also retained a higher percentage of all of their kindergarten students. Sixty-four percent of charter-school students remained at the same school until fourth grade, while 56 percent of district-school students did.

Still, the IBO report is limited to one cohort of elementary-school students, and says nothing about the attrition of older students.

Overall, students with disabilities make up about 15 percent of the charter sector and about 18 percent of students in district schools. The English-learning gap is larger, with 6 percent of charter-school students classified as English language learners, compared to 14 percent of district-school students.

IBO spokesman Doug Turetsky said the organization, charged with being a nonpartisan education watchdog, decided to revisit the report because of the volume of attention it generated last year. “We thought it would be interesting to see if the numbers had changed and fundamentally, on the broadest scale, they have not,” he said, referring to the overall retention figures.

The city teachers union is planning to release its own charter-school enrollment analysis on Thursday.