The fallout from the resignation of the Boston Latin School’s headmaster deepened Wednesday, as another top administrator resigned and unleashed a blistering critique of Superintendent Tommy Chang and Mayor Martin J. Walsh for what he called their tepid support for a school in crisis.
Assistant Headmaster Malcolm Flynn, the school’s head of discipline who has worked at Boston Latin for more than a half century, criticized the public characterization by certain black leaders that the school is a culturally dangerous and unsafe environment.
“What I am doing is telling the superintendent that I believe it was his job to get out in front and tell the truth about our school, but he didn’t,’’ Flynn, 74, said in an interview with the Globe.
The second resignation came as the school community reeled from headmaster Lynne Mooney Teta’s unexpected announcement Tuesday that she was resigning after nine years. Teta said in her resignation letter that the school and its efforts to combat racism “have been unfairly judged” by outside individuals or organizations.
“It is my belief that our school and our efforts here have been unfairly judged, for reasons that go well beyond the walls of BLS,” Teta wrote in the letter to Chang, dated June 21, which the Globe obtained Wednesday.
“It is unfortunate that at a time when Boston Latin School has made tangible progress to combat racism in our community through constructive dialogue fostered by the student body, others outside the school continue to condemn us, denounce us, and hold us responsible for district policies and practices over which the school has no control,” Teta added.
Teta, who could not be reached for comment, did not name any individuals or organizations.
Her resignation sparked questions from her supporters about whether she chose to resign or was forced out. Teta had been fending off calls for her ouster from civil rights organizations for months, insisting she was the right leader to guide the nation’s oldest school through Boston’s latest racial crisis that made national headlines.
Walsh rejected any suggestion Wednesday that he or Chang had asked Teta to resign.
“I did not ask her to step down,” Walsh said. “I did not put pressure on her.”
Walsh said he met with Teta three times since two students took to YouTube in January to allege racial discrimination at the school and inadequate responses by the administration. The mayor said he had met with Teta twice in his office in recent months and once last week during Latin School’s commencement.
“You’ll have to ask her why she turned in her resignation,” he said after an unrelated press event at City Hall. “Obviously, she had a very difficult year. That had a lot to do with it. Lynne Mooney Teta did a nice job in Latin School.”
Chang told the School Committee on Wednesday night he was surprised that Teta resigned, saying “she loved this school and was a graduate of this school.”
Teta said her resignation would be effective July 15. Chang is still identifying an interim leader and will conduct a national search for a permanent replacement.
The concerns raised by the two Latin School students — Kylie Webster-Cazeau and Meggie Noel — sparked investigations by the School Department and the office of US Attorney Carmen M. Ortiz.
The internal review found that the BLS administration properly handled six race-based incidents, but faulted the administrative team for failing to adequately address a seventh incident in which a female black student was threatened last year by a male student of another race.
In that case, the boy threatened in class to lynch the girl while holding an electrical cord and called her a racial epithet. The review faulted school administration for failing to notify the girl’s parents of the incident.
The federal investigation remains ongoing, as does a separate ongoing inquiry by the school department’s Office of Equity.
In response to the allegations, Latin School assembled an action plan to foster greater racial harmony at the school, which has already lead to a series of race dialogues with students and faculty.
Flynn submitted a three-page resignation letter to the School Department on Wednesday. The School Department confirmed that it had received Flynn’s resignation but declined to comment further.
In an interview, Flynn described a tense and torturous scene at the school, where he said in the past few weeks at least 15 to 20 teachers have been questioned by Office of Equity officials — and federal investigators — about “every little thing a student said or a teacher said.’’ Some of the complaints were five or six years old, he added.
He said he was grilled by the Office of Equity three times and spent seven hours with federal investigators, who questioned him about how he handled discipline at the school.
Flynn said he had been considering resigning for about a month. He said he shared his plans with Teta. He has been at the school for 52 years, serving 34 as an English teacher. His voice choked up as he described his decision to leave.
He made his decision, he said, because he believed the School Department and the Office of Equity have been unfairly and punitively questioning teachers and administrators. He also said Chang and Walsh did not vigorously and effectively defend against criticim that the school did nothing to address students’ complaints.
Flynn dismissed assertions that school administrators “did nothing” to discipline students or address their complaints. He said some might not have been satisfied with the discipline.
Ginny Brennan, a parent of a former Latin School student, said she thinks Teta is being unfairly blamed, noting that racial unrest unfortunately has existed across the school system for decades.
“It appalls me that Lynne Mooney Teta was thrown under the bus or is being made an example,” Brennan said. “The people who wanted to make this happen pushed and pushed. They are making someone accountable for a societal problem.”
She added, “Her departure from BLS only sends a wrong message . . . that education is about politics and not about learning.”
Civil rights activists made a push Wednesday afternoon for black community leaders to be involved in the headmaster search and stressed that all city officials should be held accountable for racial inequity in the schools.
Darnell Williams, the local Urban League president, denied that Teta was being treated as a scapegoat.
“For someone to say that [Teta] was targeted — the only thing that was targeted was her inaction,” Williams said.
Kevin Peterson, director of New Democracy Coalition, said that Teta’s assertion that the school’s efforts were unfairly judged was “absolutely unfair and false.”
As students returned to school, many said that they hoped Teta’s resignation would offer closure to a controversial chapter.
“I felt like there wasn’t a lot she could do, but she tried her best with the time she had left,” said Michael Egbueze, 15.