The Long Island Rail Road has renewed its lease with a freight rail operator later criticized by federal regulators for a safety record that includes three derailments on the LIRR’s tracks within about 16 months and a 2015 train crash in which an uncertified locomotive engineer fled the scene.

MTA president Thomas Prendergast, however, said Monday that the 10-year lease extension for New York & Atlantic Railway came before the Federal Railroad Administration “issued a report highlighting a number of serious safety concerns,” and would not be the LIRR’s final word on the matter. Metropolitan Transportation Authority officials did not rule out severing the agreement or putting the freight contract out to bid.

“In light of the FRA findings, MTA will explore all options, including how freight service on LIRR moves forward, to ensure the highest safety standards are met,” Prendergast said.

As the LIRR considers its next move, several elected officials and civic activists are calling on the commuter railroad to dump its freight partner, which over the last decade has been involved in nearly three times as many accidents or safety incidents as the national average, according to FRA stats.

Those calls come amid growing concerns over railroad safety in the region, after last month’s fatal NJ Transit train crash in Hoboken and an LIRR train collision in Garden City days later that injured 33 people.

“If they’re saying that they’re so concerned about public safety, then they need to look into this,” said Mary Parisen, chair of Civics United for Railroad Environmental Solutions, or CURES, an advocacy group that has raised concerns about NYAR’s practices for years. “They need to consider what this company is doing and how they’re operating. And, at this point, it’s not with the public in mind.”

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The FRA’s review found “several safety issues that could increase the risk of additional accidents” on LIRR’s tracks. They include failure to adequately train, test and certify train crews, dangerous conditions at grade crossings, and recordkeeping that was “so poor” investigators couldn’t figure out whether engineers were qualified to operate trains, according to the report released in September.

NYAR officials say their “top priority is safety” and that they have taken several measures to address the FRA’s concerns.

New York and Atlantic — a subsidiary of Chicago-based Anacostia Rail Holdings — has operated on LIRR tracks since 1997, when the two railroads reached an agreement under which NYAR would pay at least $12.8 million over 20 years to take over freight operations from the LIRR.

MTA officials said NYAR in June exercised its option to extend by a decade its lease, which could be automatically renewed, without a vote by the MTA board, as long as the freight company met some basic performance benchmarks.

But a number of incidents involving NYAR trains have raised concerns for years about the company’s safety practices and fitness for the contract extension, including two derailments on Long Island last year.

In one, an engineer operated a train in the wrong direction, the FRA said. In the other, the train was speeding and overloaded, according to the FRA.

Then on July 8, 2015, a NYAR train traveling above the speed limit went through the Maspeth Avenue crossing in Maspeth, Queens, before the safety gates had lowered and warning devices activated, and crashed into a tractor trailer, injuring its driver, according to the FRA.

The train’s event recorder showed that the train similarly barreled through two other crossings before the gates lowered during the same trip.

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“In the aftermath of the accident, the locomotive engineer left the scene and did not return to the railway. NYAR subsequently terminated his employment,” the FRA said in its report, which noted that the agency “was unable to reach the engineer for a post-accident interview.”

That incident sparked the federal review of NYAR’s safety practices that found that the company was not properly training and certifying train crew members and allowed engineers, including the one involved in the crash, “to operate locomotives without proper documentation demonstrating they were qualified.”

NYAR has taken steps to address the issues raised in the review, including by establishing a new engineer certification program, making various safety improvements at crossings, hiring an outside safety consultant, and improving communications with the LIRR, according to the FRA.

NYAR officials declined to be interviewed. In an email statement, however, NYAR Chief Safety and Compliance Officer Thomas Leopold said the firm will continue to fully cooperate with the FRA, even though company officials “disagree with some of the conclusions in its report.” The company did not specify the conclusions with which it disagreed.

“We perform a vital service to the flow of commerce in New York City and Long Island, and hold ourselves accountable to keep our customers, employees and the communities in which we operate safe at all times,” Leopold said in the statement.

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NYAR officials, in a statement Monday, said they appreciate MTA chief Prendergast’s safety concerns and are ‘‘in full compliance’’ with the FRA’s recommendations.

According to the FRA, New York and Atlantic Railway has been involved in 43 accidents or incidents since 2007, resulting in 26 injuries to NYAR employees. The average railroad in the same class as NYAR reported about 15 accidents/incidents during the same period.

The company reported nine accidents/incidents in 2015 — the most of any single year over the last decade—and three through July of this year.

NYAR transports 28,000 carloads of solid waste, construction and demolition material and other products through Queens, Brooklyn, Nassau and Suffolk annually. The company has been the subject of various other complaints by residents in communities through which they travel, including over noise, odor, and improperly filling and covering containers.

Since the FRA report’s release, a number of elected officials have urged the MTA to cut ties with NYAR, including Assembly members Catherine Nolan (D-Ridgewood) and Michael Miller (D-Glendale). In an Oct. 5 letter to Prendergast, Miller called the company “a danger to their employees, the LIRR infrastructure, and the communities in which they operate.”

At an MTA board meeting last month, board member Ira Greenberg, who represents the LIRR Commuter Council, called the FRA report “extremely disturbing.”

Rep. Grace Meng (D-Queens), who pushed for the FRA’s safety review of NYAR, has stopped short of calling on the LIRR to get rid of the company, but said she is “seriously considering it” given the findings of the report, including that the engineer disappeared from the scene of the Maspeth crash.

“No one can look at this report and decide, in good conscience, that they are responsible partners going forward,” Meng said.