Amtrak announced William J. Flynn will be its next CEO. He will start in April.

Flynn is currently CEO of Atlas Air Worldwide, a cargo and charter airline. Atlas also contracts with Amazon to operate some of its Amazon Air flights.

Pilots at Atlas have accused the company of relaxing training and hiring standards to meet Amazon's demand, leading to a fatal 2019 crash. Flynn denied the connection.

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Amtrak said Monday that it hired William J. Flynn, former chief executive of cargo and charter airline Atlas Air, to be its next CEO.

Flynn will replace another former airline executive, Richard Andersen, who has run the railroad since leaving Delta Air Lines in 2017.

Flynn has led Atlas Air for 13 years. While the carrier expanded under Flynn's leadership, earning lucrative contracts with companies like Amazon, as well as valuable charter customers, the carrier has been plagued by safety concerns in recent years.

In February 2019, a Boeing 767 jet flown by Atlas Air crashed while approaching Houston's George Bush Intercontinental Airport. Atlas Flight 3591 was operating under contract with Amazon as an Amazon Air flight. Both pilots, along with a Mesa Airlines pilot who was riding in the jumpseat, were killed.

Pilot error has been cited as a likely cause, but the investigation is still ongoing.

In the aftermath of the crash, numerous systemic safety concerns emerged, raised by current and former pilots, some of which have been corroborated by the National Transportation Safety Board (NTSB).

Even before the crash, several pilots told Business Insider that they thought an accident was inevitable.

Pilots flying for Amazon Air — consisting of Atlas Air and Air Transport Services Group (ATSG) crews — said that the rapid growth of Amazon's air-cargo network — operated by Atlas and ATSG — coupled with low pay, meant that inexperienced pilots were flying, despite not being adequately qualified.

Pilots and union leaders raised additional concerns surrounding shoddy training standards, fatigue and overwork, poor morale, and below-industry pay as contributing to safety risks.

In March, a month after the crash, Flynn told Business Insider in a statement that the complaints were "misleading and inaccurate, and inappropriately connect the Flight 3591 tragedy with ongoing contract negotiations."

"Since our founding over a quarter of a century ago, we have worked hard to earn and maintain a record of safety and compliance," Flynn said in the statement. "We are heartbroken by the loss of Flight 3591 that claimed the lives of three of our friends and colleagues. We are working closely with the National Transportation Safety Board and the Federal Aviation Administration (FAA) to learn what happened, why it happened and what needs to be done to prevent a recurrence."

In December, the NTSB released documents detailing numerous problems relating to Atlas' pilot hiring practices, particularly surrounding the first officer on the flight, Conrad Jules Aska. Aska was hired at Atlas despite several red flags at previous jobs.

NTSB investigators wrote, from talking with a check airman, or pilot trainer, at one of Aska's previous jobs, that, that he "was making very frantic mistakes, lots and lots of mistakes, and did a lot of things wrong but did not recognize this was a problem. He thought he was a good pilot never had any problems and thought that he should be a captain. He could not evaluate himself and see that he did not have the right stuff."

Scott Anderson, senior director of flight procedures, training, and standards at Atlas, told NTSB investigators that the airline would not have hired Aska had they known about his failures to pass trainings at those two airlines. It was not clear why the airline was not aware of the deficiencies, particularly since several failed promotional checks should had been disclosed to the FAA.

The rapid growth of Amazon's cargo network is a major contributor to the safety concerns at the carriers operating on the tech giant's behalf, experts say.

Pressure to scale quickly in order to secure business can lead to a decline in safety and hiring standards.

"I am concerned anytime that new entrants into aviation particularly carrying packages or goods enter a market where their background has been essentially trying to cut costs to make money," Jim Hall, who led the National Transportation Safety Board (NTSB) from 1994 to 2001, previously told Business Insider, referring specifically to Amazon.

"Cutting costs in aviation causes deaths and accidents."

Flynn takes over as Amtrak's finances have improved, but favorability and safety has declined.

At Amtrak, Flynn will inherit a railroad that struggled to decrease accident rates under its previous executive.

From the 2016 calendar year, before Anderson took over as CEO, through the end of 2019, total accidents reported by Amtrak increased from 69 per year to 83, according to statistics from the Federal Railroad Administration.

Anderson's tenure also included a handful of deadly crashes.

In 2017, a Cascades train in Washington derailed during its inaugural run on a new route, killing three people and injuring 65 more. And in 2018, an Amtrak Silver Star train collided with a stopped freight train in South Carolina, killing 2 and injuring 92.

Federal safety officials eventually blamed the South Carolina crash on easy-to-fix human oversights, including a lack of positive train control.

Flynn's tenure will begin at a turbulent time for Amtrak. Although the railroad's finances have improved under Andersen, partly thanks to service cuts and changes made based on his airline experience, the Trump administration's budget proposal has slashed Amtrak funding.

The railroad also faces delivery delays for crucial new trains due to poor management, and is experiencing challenges keeping service reliable despite crumbling infrastructure along the busy Northeast corridor. Amtrak owns New York's Pennsylvania Station and the Hudson River tunnels connected to it.

Various proposals have failed in recent years to fund repairs to the vital pair of single-track tunnels, which were already past their expected life-span when they were damaged by Hurricane Sandy in 2012.

Repairing the tunnels and other tracks around Penn Station will prove to be among Flynn's biggest challenges. The infrastructure is also used by New Jersey Transit and the Long Island Rail Road, posing difficulties as Amtrak is forced to work around daily commutes.

Amtrak did not immediately return a request for comment.