After a recent study found that the Bloomberg administration’s strategy of closing struggling schools didn’t hurt their students, a new report complicates that picture.

The report, released Thursday by the city’s Independent Budget Office, found that students enrolled when the closure announcements were made were less likely to graduate with a rigorous diploma and more likely to earn credit through remedial classes, at least at six large shuttered schools it examined.

Students at three of the schools — Samuel Tilden, South Shore, and Lafayette high schools, where closure announcements came in 2006 — graduated in four years at about the same rate as peers at similar schools. But at another three high schools — Bayard Rustin, Louis Brandeis, and Franklin Lane, where closure announcements came in 2007 and 2008 — students fared worse, with only about 44 percent graduating in four years, compared to 47 percent of similar students.

The IBO report also raises questions about the quality of the education those students received, whether they stayed at their closing school or transferred away.

Compared to their peers, the students from all six closing schools were more likely to graduate with local diplomas, not the more advanced Regents diplomas that have since become standard for students without disabilities.

They were also more likely to have earned class credit through “credit recovery” programs, which can be less rigorous than traditional classwork, and to have scored exactly a 55 or a 65 on their Regents exams. Those scores often raise eyebrows because they are the cutoffs for passing those tests to qualify for a local or Regents diploma.

Sarita Subramanian, the IBO analyst who wrote the report, said policymakers should note the possible negative effects of the phase-out process.

“People might think the benefits outweigh the costs” of school closures, Subramanian said. “But it’s good to know what the costs are, especially for the students enrolled at the schools.”

Subramanian cautioned that she did not examine the causes for differences in diploma types or credit recovery rates, but noted that staffers at closing schools could have felt pressure to ensure their students met graduation requirements by the time the schools dissolved.

The six high school closures the IBO analyzed were among dozens during Michael Bloomberg’s three terms as mayor. That strategy proved deeply divisive and inspired aggressive protest from the city teachers union and many parents and community groups. As students and funding left those schools, extracurricular activities, advanced classes, and school morale often disappeared as well.

Last month, the de Blasio administration announced its own plans to close three schools at the end of the school year, including one small high school. That school bears little resemblance to the large, comprehensive high schools examined in the IBO report, though, and Mayor Bill de Blasio has largely rejected school closure as a strategy for improving the city’s schools.

Instead, the city has poured additional resources into struggling schools through its “School Renewal” program, though officials have said they will move to close schools that are unable to improve.

Correction: An earlier version of this story said that two of the schools the de Blasio administration wants to close this year are high schools. Just one, Foundations Academy, is a high school.