Marshals view their jobs as critical to protecting planes and airports from terrorists. But many describe a program in crisis.

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WASHINGTON — It is supposed to be a last line of defense against a Sept. 11-style attack on the United States. But a federal program that puts armed undercover guards on commercial airliners is in such disarray that it does little to deter terrorists, many of its employees say, and is being investigated by Congress.

Alcohol abuse among some in the Federal Air Marshal Service (FAM) is so rampant that the Transportation Security Administration (TSA), which oversees the program, has had to monitor whether the armed guards show up for their flights sober, according to five people familiar with the situation. TSA said its office of inspection makes quality-assurance visits to ensure that the air marshals are properly prepared for their missions.

Female and minority air marshals said in court documents and interviews that they faced discrimination at work, including being subjected to sexually explicit messages and racist jokes and memes sent on government-issued cellphones. Other air marshals said they were fired or threatened with termination for minor infractions, while misconduct by managers was overlooked. Just 22 percent of the marshals thought their leaders maintained “high standards of honesty and integrity,” according to a federal employee survey completed last year, one of the lowest rankings among agencies.

“I ultimately decided to leave (retire) because I was denied the ability to leverage my experience for the good of the FAMs and I realize that I was part of a system which was putting the emotional well-being of FAMs at risk,” Kathleen Christian, who resigned last year as a clinical psychologist with the federal air marshals, or FAMs, said Nov. 17 in a scathing email to several marshals. A copy was obtained by The New York Times.

Congress has asked the Government Accountability Office (GAO), its investigative arm, to review the workplace complaints raised by air marshals, said Charles Young, a spokesman for the office.

Employees with the air marshals view their jobs as crucial to overall efforts to protect airplanes and airports from terrorist attacks. But interviews with more than two dozen former and current federal air marshals describe an organization in crisis.

Burnout is high. Morale is low. Some of those interviewed said they were aware of colleagues who had committed suicide or attempted it. Nearly all described having a variety of job-related health problems; one marshal said he had depression, sleep apnea and dizzy spells.

“The conditions in the air marshals make it more likely that a FAM will not react to a threat than react to one,” said Clay Biles, a former air marshal, who resigned from the agency in 2013 after a five-year stint.

Most of the current and former air marshals spoke on condition of anonymity because they were not authorized to publicly discuss operations of the security agency; some said they feared retaliation for speaking out.

The TSA declined to respond to specific questions about the complaints, but it said all allegations of misconduct are investigated.

“TSA and the Federal Air Marshal Service leadership take the care of our people very seriously and vigorously dispute any indication otherwise,” said Thomas Kelly Jr., a spokesman for the air marshals.

Kelly acknowledged that alcoholism has been a problem for some air marshals — he said about 13 marshals had gotten DUIs in the past three years — and he reported the suicide of one marshal in the past five years. But he said neither issue represented systemic problems within the program.

The federal air-marshals program was created in 1961, during the Kennedy administration, in response to an increase in airline hijackings linked to Cuba. It has since grown from about a dozen air marshals to a force that officials have said numbers about 3,000, with an $800 million annual budget to safeguard against terrorist attacks aboard domestic and international flights.

After the Sept. 11 attacks, the program was pulled into the newly created TSA and under the umbrella of the Department of Homeland Security. Since then, it has been the focus of a number of congressional investigations, internal inquiries and media reports documenting a series of scandals, including marshals hiring prostitutes and managers scheduling flights to meet up for sexual trysts.

Government reports have questioned the air marshals’ effectiveness and suggested that its budget be redirected to other counterterrorism programs. A two-paragraph unclassified statement from the Department of Homeland Security’s inspector general this past year said parts of the air-marshals program could be “discontinued” and its “funds could be put to better use.”

A report by the GAO, also published this past year, found that TSA could not accurately describe the marshals’ ability to deter terrorist attacks. “TSA does not have information on its effectiveness in doing so, nor does it have data on the deterrent effect resulting from any of its other aviation security countermeasures,” the auditors wrote.

Critics note other security measures — including fortifying cockpit doors and arming thousands of pilots — reduced in-flight threats and, in turn, made the protection provided by air marshals less necessary. TSA also has enacted stricter passenger-screening measures to prevent terrorists from boarding planes.

With a small workforce, air marshals are able to protect only a small fraction of the more than 42,000 flights in the United States each day. There were no air marshals aboard the trans-Atlantic flight carrying the shoe bomber Richard C. Reid in December 2001, nor the one carrying the underwear bomber Umar Farouk Abdulmutallab in December 2009. Both men were linked to al-Qaida.

Rep. John Duncan Jr., R-Tenn., a longtime critic of the air-marshals program, said the agency averaged one arrest each year per 1,000 marshals. Most of those arrests were for rowdy passengers or immigration violations, according to several air marshals.

Instead of putting marshals on flights deemed to be the highest risk, they are spread across as many flights as possible, including on domestic regional 50-seat planes. The strategy has been ridiculed as “flights to nowhere” by the Air Marshal Association, a union that is pushing the Senate to approve a bill requiring that air marshals be assigned to higher-risk flights. (It already has passed the House.)

“Based on how the program is run now, most of what the air marshals do is just security theater — it serves absolutely no purpose other than showing that they are doing something,” said Robert MacLean, an air marshal who was fired by TSA in 2006 after disclosing to an MSNBC reporter that the agency was planning to reduce the number of air marshals on overnight flights. He was rehired after a nearly 10-year battle that reached the Supreme Court.

Air marshals interviewed for this article said their biggest problem was the number of hours they were expected to fly. They are not allowed to sleep on flights, and back-to-back international trips involving prolonged periods of sitting awake take a toll. Several air marshals said they took medication or drank alcohol to stay awake — despite a policy prohibiting alcohol consumption within 10 hours before work.

The agency said it had begun an alcohol-awareness program, but several air marshals said it has had little effect. One marshal who was a recovering alcoholic and featured in an awareness video later took his life, according to two employees. The agency declined to comment, and the employees said the video was not being released.

Air marshals blamed their lack of sleep for losing their weapons or leaving them where passengers could find them. It is unclear how often this has happened, but in one case this past year, operations at Indianapolis International Airport were shut down for several hours after a marshal lost his weapon.

Air marshals also blame management, which they said had turned a blind eye to their concerns, including complaints about being subjected to sexist and racist behavior at work.

Several air marshals have asked Congress to remove the program from TSA’s purview and entrust it to a different agency, like Customs and Border Protection or the Federal Bureau of Investigation.

“TSA is just not capable of overseeing the federal air marshals because it’s not a law-enforcement agency,” MacLean said. “The past 15 years or so have shown that.”