The groups, including the Lawyers Committee for Civil Rights and Economic Justice, allege in the lawsuit that the school system and Superintendent Tommy Chang have a "disturbing practice" of giving student information to immigration authorities.
Chang told the Boston Globe on Friday that he's agreed to step down as superintendent after three years, but declined to discuss the circumstances of his departure.
The lawsuit stems from the deportation of an East Boston High School student. The lawsuit says evidence used by federal officials in deportation proceedings included a school report about two students who tried unsuccessfully to start a fight.
The school's incident report included unsubstantiated allegations of gang involvement, according to the lawsuit.
The school shared the report with the Boston Regional Intelligence Center, a collaboration of local, state, and federal law enforcement agencies that includes Immigration and Customs Enforcement agents.
The student was held in custody for more than 16 months before being deported, the lawsuit said.
East Boston is a hotbed of activity for the violent MS-13 gang, federal authorities have said.
"The issue of public schools' cooperation with law enforcement - already of intense public importance - has taken on heightened urgency for immigrant families since 2017," the lawsuit says. "As federal deportation efforts intensify, the question of how and under what circumstances public schools are providing information to the U.S. Department of Homeland Security Immigration and Customs Enforcement has become even more crucial."
Chang has previously said the schools don't share student information.
A schools spokesman said he could not comment.
"Neither the city of Boston nor Boston Public Schools have been served with the lawsuit," spokesman Dan O'Brien said. "Boston Public Schools will review the lawsuit once it is received."
Copyright 2018 The Associated Press. All rights reserved. This material may not be published, broadcast, rewritten or redistributed.