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Another top Boston Latin School administrator resigned Wednesday, unleashing a blistering critique of Superintendent Tommy Chang and Mayor Martin J. Walsh for what he described as their tepid support for a school in crisis.

Assistant Headmaster Malcolm Flynn, the dean of discipline who has worked at the school for more than a half century, criticized public characterization by certain civil rights leaders that Latin School is a culturally dangerous and unsafe environment.

“That kind of stuff is untrue,’’ Flynn said in an interview with the Globe.

Flynn, 74, said he submitted a three-page resignation letter to the School Department around 5:30 Wednesday in which he outlined his utter disappointment in Chang.

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“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 said. “He should have been out front’’ on this.

Flynn quit one day after the surprise resignation of headmaster Lynn Mooney Teta.

The School Department confirmed that it had received Flynn’s registration but declined to comment further.

Controversy in the school began in January, after a pair of black students took to YouTube to allege that racism simmers in the nation’s oldest school. The students had alleged that Mooney Teta did nothing to address the tense racial climate at the school.

Their video sparked a public outcry, with civil rights leaders demanding that Mooney Teta step down and urging a federal investigation.

The US Justice Department and the School Department’s Office of Equity — which had investigated the allegations last year — began investigating. Other students and their parents began complaining.

Flynn said critics of the school demanding resignations have never been there and decided as soon as the issue came up that the only solution was to remove the administrators.

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Flynn described a tense and torturous scene at the school in the past several weeks, where he said that 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.

Latin School fosters vigorous classroom discussions about thorny issues, including those involving racism, which might produce statements others consider offensive, he said.

He — like the teachers and other administrators — said he was grilled by 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 and that he had shared his plans with Teta — who, he said, had been under a gag order and forbidden from speaking to the press.

Flynn has been at the school for 52 years, including 34 as an English teacher. His voice choked up as he described his decision to leave.

“My decision today was a big surprise to a lot of people,’’ he said.

Flynn said he is quitting because he believes the School Department and the Office of Equity have been unfairly and punitively questioning teachers and administrators. He also said the superintendent and mayor did not vigorously and effectively defend against criticim that the school did nothing to address the students’ complaints.

Flynn praised Teta for creating a series of school discussions that would help students voice their concerns.

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Earlier in the year, the equity office reported that school administrators acted appropriately in all but one of the cases investigated in a one-year period that began November 2014. But black leaders and some parents felt that the probe did not go far enough.

Flynn dismissed assertions that Latin School’s administrators “did nothing” to discipline or address the complaints. He said school disciplined the students involved, but argued that some might not have been satisfied with the discipline.

One case involved a girl who alleged another student threatened to lynch her. The girl recalled the incident seven months after it occurred.

“The student was disciplined,’’ he said, adding that he could not detail what action was taken because of student privacy records. “But it was determined [by some] that it was mishandled.

“That could be said about a lot of things,’’ he added. “That by itself does not mean that we are creating the most dangerous school in America.”


Meghan E. Irons can be reached at meghan.irons@globe.com. Follow her on Twitter @meghanirons.