The study's authors said they believed more children were somehow gaining access to handguns without supervision, allowing them to turn what might have been small acts of aggression into massacres.
Still, the researchers at the Centers for Disease Control and Prevention said schools remain safe.
"The risk for violent death that a child faces at school is less than one in a million," said Dr. Mark Anderson, an epidemiologist with the CDC's National Center for Injury Prevention and Control.
The study found that violent deaths at school - including slayings and suicides - dropped by 43 percent from the 1992-93 school year to 1998-99.
During the same time, the rate of deadly attacks with more than one victim rose steadily. In 1992-93, there were no multiple-victim school slayings, but by 1998-99 they accounted for 42 percent of all violent deaths at school.
More than two-thirds of the slayings were carried out with firearms, usually handguns. About 14 percent used knives, about 6 percent were beatings and a smaller number used strangulation or some other method.
Nearly all the suicides - 90 percent - were carried out with guns.
The CDC collaborated with the Justice Department and the Education Department on the study. The results are reported in Wednesday's Journal of the American Medical Association.
Using newspaper clippings and interviews with police, the authors collected information on 172 slayings and 30 suicides, including 11 combination homicide-suicides, at elementary, middle and high schools.
"We also found that ... the perpetrators or offenders who committed these acts were more likely to have been bullied in the past and also more likely to have expressed some type of suicidal behavior, such as writing a note or even carrying out a plan for suicide," Anderson said.
The most notorious recent outbreak of school violence was the April 20, 1999, massacre at Columbine High School in Colorado in which a pair of students murdered 12 pupils and a teacher before taking their own lives.
Last week, Massachusetts authorities apparently thwarted a planned Columbine-style assault by local high school students.
The report urged school administrators to look at programs used in Europe that have proven effective in reducing bullying. Parents and teachers should also be on the alert for students showing any type of suicidal behavior.
Among the findings: Most killings at school happen at the beginning or end of the school day or at lunch, when children are more likely to be crowded together and under less supervision.
"It's not overcrowding in schools we're talking about," said Bill Modzeleski, who heads the Education Department's Safe and Drug-Free Schools Program. "At any school environment what happens is that kids pour out of classroms, and they tend to congregate in groups."
The researchers also found African-American students were nearly three times as likely as white students to have experienced a violent death at school.
The attackers were much more likely than their victims to have been suicidal, to have a criminal record, to have been a gang member, or to have been associated with "high-risk" peers or have a reputation as a "loner," the study said.
They were also twice as likely than their victims to have been bullied.
A school-related violent death was defined as one that happened at school, on the way to or from school or at an off-campus school function.
In one-third of the violent outbursts, a direct threat had been made by the perpetrator. Others were preceded by a more vague signal, like a desperate note or journal entry.
© MMI, CBS Worldwide Inc. All Rights Reserved. This material may not be published, broadcast, rewritten, or redistributed. The Associated Press and Reuters Limited contributed to this report