Young black males in Boston are being dumped in special education classes and separated from their classmates at an alarming rate, a stunning new report out today reveals, prompting minority leaders to call for immediate reforms.

“It’s an unintentional consequence of bad policies,” said Najma Nazy’at, director of the Boston-area Youth Organizing Project. “I believe that how it happens here is through pushing out the young people who they just assume are going to create the most problems.”

The “Opportunity and Equity” report — released this morning by Boston Public Schools, the Annenberg Institute for School Reform, and the Center for Collaborative Education — found that nearly 40 percent of black boys with disabilities at the elementary level are being taught outside of mainstream classrooms.

The report found black male students were placed in separate classrooms at almost twice the rate of white males, and Latino males at 1.6 times the rate of whites.

The 261-page report analyzed data on 88,000 Boston students and points to “staggering” disparities in the graduation rates of blacks and Latinos compared with whites and Asians, and has prompted the head of the NAACP’s Boston chapter to request a meeting with Mayor Martin J. Walsh and school ?officials.

“It does concern us that so many of our kids are identified as special needs when we know there is no difference between a child of color and a white child if they’re afforded the same opportunities,” NAACP Boston President Michael Curry said.

The new report links its findings with research that shows special education students who are kept in general education settings perform better on reading and math tests, make better grades, are more academically engaged, and have “ultimately, better opportunities in adult life.”

Special education classes are also more costly — with Boston Public Schools needing $6 million in extra funding last year because of an increase of students with disabilities.

The report recommends the district “review special education identification and placement policies and procedures with an eye toward correcting gender and racial/ethnic biases.”

Interim school Superintendent John McDonough acknowledged that the process needs to be re-examined.

“It is not our belief that students of color have more disabilities than students who are not of color,” McDonough said. “We now have a challenge to look deeper than the finding and ask those questions about both practice as well as causality. … I want to be very clear, this is not about deficiencies in students. We own this.”

The Herald reported in July that Boston has also used special education classes as dumping grounds for non-English-speaking immigrant students and that The U.S. Department of Justice has been monitoring the district since 2010 for incorrectly placing non-English speakers.