Richmond Public Schools — dominated by African-American administrators and teachers — is being accused of fueling the “school-to-prison pipeline” through a regime of discipline that punishes mostly African-American students, particularly those with disabilities.

The claim that African-American students unfairly and illegally bear the brunt of school discipline — and the resulting disruption to their education — is included in a 28-page complaint the Richmond Branch NAACP and two African-American students filed Wednesday with the U.S. Department of Education’s Office of Civil Rights.

The goal: To gain reforms that will lead the school district to “adopt strategies that improve the school climate and ensure discipline policies that are fair for all students,” said Lynetta Thompson, president of the Richmond NAACP.

Data included with the complaint indicate that during the 2014-15 school year, more than 3,200 students in kindergarten through 12th grade were punished with one or more short-term suspensions of three to five days. Nearly 500 students were hit with long-term suspensions of 10 or more days, while 35 students were expelled, according to the complaint.

While African-American students made up 76 percent of the RPS 23,000 student population during the 2014-15 school year, 93 percent of short-term suspensions, 98 percent of long-term suspensions and 97 percent of expulsions involved African-American students, according to the complaint.

In addition, students with disabilities were nearly three times more likely to face suspensions than students without disabilities.

“There is overwhelming evidence that the school division’s discipline policies are excessively punitive and lack clear standards,” according to Rachel Deane of the Legal Aid Justice Center, which along with the ACLU of Virginia, is representing the complainants.

“Overly punitive discipline policies damage the learning environment, deny African-American students and students with disabilities of their right to an education and push children into the school-to-prison pipeline,” according to Leslie Mehta, legal director of the ACLU of Virginia.

The concern about RPS’ discipline policies hits a school district already facing major challenges. Not only is RPS a state leader in high school dropouts, it also ranks among the worst school districts in the state for student achievement scores on state Standards of Learning tests.

In a statement issued on behalf of Superintendent Dana T. Bedden, the school system pledged to cooperate with any federal probe resulting from the complaint, but also noted that concerns about discipline already are being addressed.

Expressing disappointment that the complaint was not brought first to RPS for resolution, the statement noted that “Richmond Public Schools is working diligently to ensure all disciplinary actions are fair and consistent.”

Among other things, RPS has ended zero-tolerance policies and overhauled the Student Code of Responsible Ethics. In addition, RPS stated that the system of discipline has been revamped to take into account “the nature and seriousness of the violation, the student’s age, the student’s previous disciplinary record and any other relevant circumstances in determining the most appropriate school interventions or consequences based on each student’s grade level and behavior.”

Despite the rarity of a majority-black school division being accused of racial bias, Richmond’s discipline situation is not that unusual. A recent report by the Legal Aid Justice Center contains data showing African-American students receive more discipline, are hit with more suspensions and receive more referrals to courts than any other racial group of students in Virginia. The report finds that pattern exists in virtually every school division with large numbers of African-American students.

However, Ms. Deane said Richmond became the target of this complaint because it is a standout for the number of African-American and disabled students who are impacted by discipline compared with their peers, “disparities that cannot be explained by differences in student behavior.”

A Richmond student is two times more likely to be suspended short-term than a student who misbehaves in neighboring Chesterfield and Henrico counties. RPS’ long-term suspension rate is more than 35 percent higher than the rates for the two county school systems.

The story of one of the students who filed the claim reflects what the petitioners see as an out-of-control discipline system.

Identified as J.R. in the complaint, the 13-year-old special education student ended up being restrained by school security and handcuffed by police officers who arrived later.

His crime: Agreeing to a teacher’s request to be a classroom helper.

According to the complaint, J.R. was still working in the classroom when the teacher who assigned him the tasks left.

When another teacher arrived, she confronted him and ordered him out. Seeking to find the first teacher to get a required hall pass, he then was confronted by a security officer who demanded to know why he was in the hall, moved him into a classroom and ended up putting him on the floor when the frustrated child balled his fists.

Booted from Boushall Middle School with little explanation to him or his mother, J.R. spent 13 days without any services, though RPS promises to provide home-based instruction to suspended students.

He later was assigned to the Richmond Alternative School, where he was put into a classroom by himself. He then was sent home because the counselor who was supposed to be in the classroom with him failed to show up.

He started receiving home-based instruction a month after being suspended, but was recommended for expulsion because of the claim he had tried to fight the security guard. He and his mother appealed, and the expulsion decision was overturned. He will start eighth-grade in two weeks when city schools reopen.

Ms. Deane and others believe his case raises serious questions about the treatment of students in Richmond schools.