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The former chief safety officer of the Massachusetts Bay Transportation Authority says the agency fired him in retaliation after he called attention to serious safety hazards and pushed executives to stop suppressing information about dangerous mishaps, according to a federal complaint filed in May and obtained by the Globe.

Ron Nickle, the MBTA’s top safety official for almost eight years, told the Federal Transit Administration that a top MBTA employee urged the safety department to alter an investigative report related to a 2015 runaway Red Line train, a high-profile incident that embarrassed the agency. In his 97-page federal complaint, Nickle alleged the MBTA also pressured the commuter rail system to put a premium on on-time performance, not safety.

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The MBTA has denied Nickle’s claims, saying he is misrepresenting events.

Nickle said he was fired in March as he investigated several accidents, including a worker’s electrocution on the Orange Line, a commuter rail train that had lost its wheel mid-commute, and a Green Line derailment during the Patriots’ Super Bowl parade, among others.

“I believe efforts were exerted to undermine my authority, responsibilities, obligations, and duties as a Chief Safety Officer while actively dealing with major safety concerns on the [Green Line extension] project, and serious violations of federal safety laws, rules and regulations,” he wrote in the complaint.

He alleged that he was terminated, in part, because he had met with federal regulators about such incidents and that MBTA officials chafed at his criticisms and outspoken nature.

When contacted by the Globe, Nickle declined to comment on the record, saying that the matter is under investigation. Through his attorney, Charles Goetsch, he said he had been fired because he “invited scrutiny to the T’s safety record and culture.”

The MBTA’s spokesman, Joe Pesaturo, did not answer questions about the reason for Nickle’s departure. But he said the agency has hired a new chief safety officer “to ensure the T’s Safety Department remains focused on its mission with the highest level of professionalism, expertise, thoroughness, and accuracy that its customers and employees expect.”

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“While the former employee’s statement is replete with mischaracterizations and falsehoods, the MBTA, nonetheless, will review the former employee’s unsubstantiated claims with its regulatory partners,” Pesaturo said in a statement.

The Federal Transit Administration, which regulates public transit agencies, declined to confirm or deny that it had received Nickle’s complaint.

Information about safety concerns would be treated as confidential under laws that protect whistle-blowers, according to the agency. The agency could investigate the issue and could refer the matter to the US Department of Transportation’s Office of the Inspector General.

Goetsch, Nickle’s attorney, said that Nickle filed a whistle-blower complaint in June with the Occupational Safety and Health Administration to protect himself from retaliation. OSHA said it would neither confirm nor deny such filings.

The accusations come as the T faces widespread criticism. A June 11 derailment on the Red Line crushed commutes, and delays still persist. In response, politicians and disgruntled customers launched protests against a 6 percent fare hike that went into effect July 1.

As business leaders in the region said the events pointed to a transit crisis, Governor Charlie Baker announced plans to seek more state spending on long-term improvements for the transit system.

The derailments have put the spotlight on the troubling safety record at the agency, which has a $2 billion annual budget. Over the last five years, the MBTA has had the second-highest total number of derailments of any transit system in the country, according to federal statistics.

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Paul Regan, executive director of the MBTA Advisory Board, which represents the cities and towns the MBTA serves, said the public should demand that the T respond to Nickle’s allegations.

“Any vehicle that is operating on the MBTA potentially has hundreds of lives on the line,” he said. “They need to demonstrate that these operations are safe.”

Nickle began working at the MBTA in the fall of 2011, under then-acting general manager Jonathan Davis. A few weeks after he began, Davis spoke glowingly about the steps Nickle was taking to improve the safety department, according to notes of MassDOT board meetings.

In the statement he provided to the Federal Transit Administration, Nickle said that officials told him he was let go “due to loss of confidence,” but he noted that his last performance evaluation, in 2014, had been positive.

In his complaint, Nickle mentions a February 2019 derailment on the Green Line that occurred during the Patriots’ parade. He said regular inspections should have discovered that long-term conditions on the track had helped lead to the derailment. But Nickle alleged that Jeffrey Gonneville, the T’s deputy general manager, and his investigators wanted to misrepresent or omit some findings from reports “out of fear that [the] MBTA would come under criticism by [regulators] or the public.”

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Nickle’s statement said he was told repeatedly to avoid blaming systemic problems for safety violations that affected commutes. When a Red Line train ran along the tracks without a driver in December 2015, MBTA officials revealed that an employee had jury-rigged a cord around the train’s throttle to override safety controls.

In public, officials had insisted the practice was exceedingly rare. But in his statement, Nickle said he had interviewed several employees who said it had been relatively common — and that Gonneville told him to “be careful” about revealing such information in a report.

Nickle said that both Gonneville and Brian Cristy, a director at the Department of Public Utilities, “undermined investigation findings, hazards, corrective [action] plans, with intent to limit, misrepresent, or withhold such information from the FTA and public.”

A spokesperson for the Department of Public Utilities declined to comment, referring instead to the T’s statement.

A former state transportation secretary, James Aloisi, said Nickle’s claims should be vetted, but added he’s skeptical of accusations that place blame for the T’s woes with Gonneville and other managers.

“The T has safety issues because it lacks the fiscal and human resources to make improvements,” he said. “This is not a personal failure on the part of any individual.”

Nickle’s portrait of the agency depicts leaders who allegedly operated in fear of unfavorable media coverage and frequently used the threat of reporting safety violations as a way to intimidate employees.

This fear allegedly included one of the recent general managers, according to his complaint: Nickle accused former general manager Luis Ramirez, who abruptly left the organization in December after just 15 months, of suggesting that Nickle avoid using written methods of communication “so as to avoid public, media, and regulatory scrutiny.”

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The direction came after Nickle’s e-mails were quoted in a story in the media.

“The [general manager’s] directive seriously impacted and complicated my ability to communicate and document [chief safety officer] safety activities, and made it even more difficult to communicate safety risks and perils to management and the GM,” he wrote.

Ramirez said he had no comment on the allegations.

Nicole Dungca can be reached at nicole.dungca@globe.com. Follow her on Twitter @ndungca. Vernal Coleman can be reached at vernal.coleman@globe.com. Follow him on Twitter @vernalcoleman.