The Obama administration wants to end the apparent disparities in how students of different races are punished for violating school rules.
More than half of students in school-related arrests or referred to law enforcement were Hispanic or black, civil rights data show.
"In short, racial discrimination in school discipline is a real problem," according to a letter sent to schools.
Civil rights advocates have long said that a "school-to-prison" pipeline relates to overly zealous school discipline policies targeting black and Hispanic students that bring them out of school and into the court system.
The recommendations being issued Wednesday encourage schools to ensure that all personnel are trained in classroom management, conflict resolution and approaches to de-escalate classroom disruptions.
In U.S. schools, black students without disabilities were more than three times as likely as whites to be expelled or suspended, according to government civil rights data collection from 2011-2012. Although black students made up 15 percent of students in the data collection, they made up more than a third of students suspended once, 44 percent of those suspended more than once and more than a third of students expelled.
Attorney General Eric Holder said the problem often relates to well intentioned "zero-tolerance" policies that include swift punishment for offenses such as truancy, smoking or carrying a weapon.
"Ordinary troublemaking can sometimes provoke responses that are overly severe," Holder said. He was interviewed on Tuesday on the Rev. Al Sharpton's radio show.
The government encourages schools to collect and monitor data that security or police officers take to ensure nondiscrimination.
The recommendations are nonbinding.
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