One day last fall, a 13-year-old from Woodbridge threw his lunch and became disrespectful at PACE East, a school program in Prince William County for students with disabilities.

School officials left the boy in a small, empty room as part of a process that kept him out of class for nearly three hours, attorneys for his family say.

It was not the first time the student had been secluded — and it was not unusual at PACE East, according to a complaint that the family’s attorneys filed last week with the U.S. Department of Education’s Office of Civil Rights.

The complaint, alleging discrimination on the basis of emotional disability, asserts that staff at PACE East relied too frequently on seclusion at the Manassas area school, with students missing long periods of instruction. It also alleges that school officials too often resorted to the use of physical restraint, with some students held facedown on the floor.

This happened “even when they presented no apparent threat to the safety” of school personnel, themselves or other students, it said.

Many educators say such practices are necessary in emergencies to ensure safety. They are often, but not exclusively, used with students who have disabilities and are frequently controversial.

This year, new federal guidelines urged that restraint and seclusion be used only when there is imminent danger of serious physical harm to a child or others. A 2009 Government Accountability Office report examined allegations and cases of student deaths and injuries from such practices.

In Prince William, James E. Fagan III, an attorney for the school system, said officials received the complaint last week and have begun to review it. Federal officials have not yet contacted the school system, he said.

“These are allegations of a serious nature, and we take them very seriously,” Fagan said. “Rest assured, we don’t bury our head in the sand.”

School system officials cannot comment on any specifics, Fagan said, but he noted that Prince William has “well-developed” policies concerning restraint and seclusion that the county updated last year.

“We are constantly monitoring the law in this area and training our folks in best practices, and we’ll continue to do so,” Fagan said.

The complaint cites numerous incidents at PACE East, including one in December 2011, when a student refused to leave a bus and was taken to the “quiet room” in a process that lasted nearly five hours. The complaint indicates that the student “wet himself.”

The complaint cites a school log that refers to 115 cases of restraint and 147 instances of seclusion at PACE East between September 2011 and March 2012. Periods out of class lasted as long as six hours for conduct including class disruption, profanity, refusing to follow directions, running away, and hitting and kicking staff, according to the complaint.

“Restraint and seclusion are supposed to be used as a last resort,” said William B. Reichhardt, the lead attorney in the case, which was filed jointly by two law firms and the Legal Aid Justice Center.

At the Prince William program, it became a “default” option, he said.

Prince William’s written policies say that physical restraint or seclusion should be used only “under circumstances which create emergency situations” and when other options have failed or are not possible.

In the quiet room, behavior is supposed to be recorded at one-minute intervals, with the door opened for checks and left open once a student is calm, according to the policies.

Attorneys who filed the complaint said it is impossible to tell exactly how much time students spent in the PACE East quiet room — which one described as the size of a walk-in closet — but contend that the log suggests “an abuse of that mechanism.” In some cases, the log suggests that the door to the room is left open.

Not all school systems use seclusion rooms.

In Loudoun County, no such room exists, and only one case of seclusion occurred there last school year, spokesman Wayde Byard said. In Prince George’s County, seclusion is not used, spokesman Briant Coleman said.

In Fairfax County, spokesman John Torre said 11 schools have seclusion rooms but students are placed in them for safety reasons and in cases of immediate danger, not to manage behavior, and only after other options have failed.

Federal officials said the Prince William complaint is being reviewed. During the past 26 months, 71 complaints charging discrimination based on disability have been filed with the Education Department’s civil rights office, spokesman Daren Briscoe said.

Federal education data released earlier this year showed that 70 percent of physical restraint cases in schools involved students with disabilities, a group that accounted for 12 percent of students in the survey.

“It’s quite widespread, and it has been for a long time,” said Reece L. Peterson, a professor of special education at the University of Nebraska in Lincoln who studies the issue. Part of the problem, he said, appears to be a lack of training in schools.

Student behavior can be challenging, he said, ranging from minor classroom issues to violent outbursts. “Many educators are frustrated from time to time and often don’t have the skills or background or training to deal with it,” he said.

Lately, Peterson said, a perfect storm has developed around seclusion and restraint: Financially strapped schools having less money to do training, which may increase problems. Alarmed parents have been sharing their experiences through social media.

In Washington state, an uproar started in late November after a parent posted photos of a padded, booth-size seclusion room on her Facebook page.

The complaint from Prince William lists a dozen instances during which the Woodbridge student — who has substantial emotional disabilities, his attorneys say — faced some form of restraint or seclusion.

In one incident, he was turning around in his seat and talking in a special crisis area. When told to be quiet, he threw a pencil bag, just missing the head of a staff member. Two staffers physically restrained him and took him to the quiet room, but he struggled violently. His mother “arrived at the school to find her child prone, in handcuffs, being arrested by police,” the complaint says.

The boy’s mother, whom The Washington Post is not identifying to protect her teenage son’s privacy, said the school’s approach worsened her son’s difficulties. He is now placed at a different school outside of the county.

In an interview through an interpreter, she reflected: “He felt very, very depressive.”

The complaint asks for a special master to oversee a plan to overhaul the system of behavior interventions at PACE East. It asks that staff receive more oversight and training in “de-escalation techniques” and that psychological services be provided for students who need them.