A new 7000-series train prepares to depart from the Pentagon Metro Station on April 14 in Arlington. (Matt McClain/The Washington Post)

Metro’s central train control center — tasked with ensuring the safety of thousands of passengers moving through the nation’s second-busiest rail system — is chronically understaffed, chaotic and filled with distractions, according to a federal report released Wednesday.

Staff members lack adequate training and have no formal checklists to help guide them in doing their jobs. Employees frequently ignore rules — several were seen using cellphones while working. And in other instances, because of miscommunication trains were directed into areas that should have been off-limits.

These findings and other observations are part of an unprecedented federal safety inspection of operations at the Washington Metropolitan Area Transit Authority.

Officials with the Federal Transit Administration initiated the review after a fatal Jan. 12 smoke incident in which the meltdown of track-based electrical components filled a Yellow Line tunnel with smoke just south of the L’Enfant Plaza station. One woman died, and more than 80 riders were sickened. Congress gave the FTA new authority to conduct such inspections in 2012.

The 116-page Safety Management Inspection report paints a troubling picture of WMATA, saying it has failed to follow through on efforts to improve safety since the 2009 Red Line crash that killed nine people.

“These are serious findings that strongly indicate that, despite gains made since the Fort Totten accident, WMATA’s safety program is inadequate,” said U.S. Secretary of Transportation Anthony Foxx.

Acting FTA Administrator Therese W. McMillan said the report is an “important wake-up call” for WMATA.

“Since Fort Totten, Metro has made important progress,” she said, adding that Metro has a safety foundation in place that it didn’t have before the 2009 Red Line crash. “What they lack is effective execution.”

Metro officials declined to discuss the report, issuing only a prepared statement. A spokeswoman said Wednesday that Jack Requa, the interim general manager, was not available for interviews Wednesday.

“We welcome this report as a road map for continuous safety improvements at Metro, and we especially appreciate the recognition of the many actions that we have taken to date to provide a foundation for our future work,” Requa said in the statement.

“We will strengthen our operations, customer service and safety culture through training, staffing and ensuring compliance of safety policies and procedures. And with the understanding of our customers, we will address the need for a better balance between service and track outages to upgrade the system. We remain committed to creating an even safer system.”

Despite her agency’s findings, McMillan sought to reassure Metro customers.

“WMATA is not unsafe,” she said. “Today’s findings should not be interpreted as a reason for WMATA’s rail and bus passengers to seek other means of transportation. However, WMATA must do better to improve its safety performance.”

As part of their review, FTA officials interviewed more than 300 people, from the authority’s top executives to frontline staff. Officials reviewed safety oversight systems for bus and rail operations.

They identified issues related to Metro’s bus system, but the majority of their concerns were with Metro’s rail operations — in particular, the central train control center known as the Rail Operations Control Center (ROCC).

The ROCC is akin to the system for managing the nation’s air traffic, but WMATA controllers are responsible for managing the movement of more than 100 trains.

The federal review found shortcomings in virtually all aspects of the center’s operations, including training, management and documentation. The findings are significant, officials note, because problems in the ROCC ripple through all parts of the rail system.

“These issues significantly impact the ability of the Metrorail system to schedule and conduct maintenance work [and] manage abnormal and emergency events,” the report said.

Officials found that Metro’s 34 train controllers fill what is “arguably the most challenging job at WMATA, providing 24 hour, seven-day-a-week coverage,” but that number is 20 short of the 54 controllers authorized by the transit authority. As a result, the staff might work six or seven 12-hour days per week, and even then, supervisors sometimes struggle to fill all shifts.

Further complicating their work, Metro controllers are asked to do tasks beyond what is required of those who work in similar jobs in other transit systems. Officials also identified problems with the computer software system used in the ROCC, echoing a Washington Post report that found the agency’s computer software is outmoded and generates so many needless alarms that warnings about smoke and other problems sometimes go unheeded by controllers.

Efforts to revamp the system, however, have stalled.

Even when controllers are on the job, the inspection found, it’s not clear that they are always focused on managing the trains. Officials noted that they often saw controllers using their cellphones while on duty, a violation of policy.

The report also cites a high level of noise and distraction in the ROCC that contributes to errors, including instances in which trains were routed into active work zones and train operators violated red signals after miscommunication from controllers.

Among other findings in the report, officials said that Metro is hobbled by outdated computer systems that hinder its ability to keep accurate records. The transit authority also struggles to balance the needs of its customers with the need to maintain the system and make critical safety repairs. The report noted that WMATA has pulled back on the amount of time crews can access the system so it can “expand service and reduce customer inconvenience,” but federal officials said that may be hampering Metro’s ability to make repairs.

Officials found that WMATA’s maintenance departments must constantly reschedule work because they can’t get the necessary access to make needed repairs. As a result, there is a growing backlog of work dating back as far as 2012.

The FTA inspection report is the result of just one of a series of ongoing reviews of WMATA’s operations since the fatal incident in January and revelations that the authority mishandled millions in federal grant money.

Next week, the National Transportation Safety Board is scheduled to hold two days of hearings on the Jan. 12 incident. The Government Accountability Office also is reviewing Metro operations, and a group of transit experts — assembled by the American Public Transportation Association — is examining the ROCC.

McMillan said that although the public may be troubled by the FTA’s findings, cutting funding is not the answer.

“You cannot starve a transit agency into safety compliance or a state of good repair,” she said. “It is important that the federal government be a partner.”

Implementing FTA’s directives will “not be easy, cheap, fast or free,” said Sen. Timothy M. Kaine (D-Va.). “The worst thing would be to starve Metro.”

Even so, the region’s congressional delegation said that although they support fully funding Metro, those dollars will come with strings.

As part of the report, FTA officials issued 78 corrective actions needed for the Metrorail system and 13 corrective actions for the Metrobus system. Metro has 30 days to respond. Within 60 days, Metro officials must submit a plan to the FTA for addressing those corrective actions.

Said Virginia Sen. Mark R. Warner (D): “Metro should expect continued robust congressional oversight of its safety and operations.”

Faiz Siddiqui contributed to this report.