After a legal threat and a prolonged negotiation, Boston Public Schools officials this month committed to a new regime of student discipline: The district will no longer suspend students in kindergarten, first, and second grades.

WBUR reporting found that more than 600 kindergartners were suspended in Massachusetts in 2014-15.

Under the agreement, the city schools will also block suspensions for third to fifth graders starting next school year except in cases where those students have committed misconduct such as “serious physical harm,” bringing a weapon to school, or repeated bullying.

The district also pledged to train all educational staff on the negative effects suspensions have on student learning and on alternative “non-exclusionary” approaches to discipline.

In a statement, interim superintendent Laura Perille thanked Greater Boston Legal Services (GBLS) for working with the district on the new policies, and promised to follow through on “full implementation of disciplinary protocols” with staff.

The changes were in response to a threatened challenge from GBLS, which represents low-income clients.

The official rate of suspensions at Boston Public Schools has been dropping in recent years: from 6.2 percent of students in the 2012-13 school year to 3.8 percent in 2016-17.

But a complaint finalized by GBLS in early 2017 alleged that that was only half the story. “All levels of BPS educational staff ... routinely call parents and instruct them to pick students up early,” the complaint alleged. “If parents refuse, school leaders attempt to persuade, intimidate, or bully parents into compliance.”

Elizabeth McIntyre led this effort as part of GBLS’s School To Prison Pipeline Intervention Project. She said it sometimes took the form of escalating threats to parents: “ ‘You have to come pick them up, or I’m gonna call the police.’ ‘You have to come pick them up, or I’m gonna call an ambulance.’”

Because this off-the-books process occurs without a suspension hearing or written notice of the action, GBLS argued that it is in violation of state law.

McIntyre said that she was “very impressed” with the way the district handled their complaint: agreeing to change its processes and guidance before the matter went to court. They negotiated for a year and a half over the provisions in a Nov. 16 settlement.

McIntyre, who observed “unlawful suspensions” at more than 40 of Boston’s 125 public schools, said she hopes this agreement can be reproduced in other districts relying on this practice.

As it pressed its complaint, GBLS represented 283 students who had been unlawfully suspended since 2014. All were students of color and all were low-income.

This story was first published by WBUR 90.9FM on Nov. 16. The Reporter and WBUR are in a partnership by which the news organizations share resources.