Officials at the Washington Area Metropolitan Transit Agency have submitted their responses to a sharply critical report by the Federal Transit Administration that found troubling gaps in the agency’s safety management and employee training programs, including instances where employees tasked with managing subway trains were spotted using their cellphones while on the job.

“We provided our draft comments to FTA ahead of the 30-day deadline and in compliance with their directive,” said Metro spokeswoman Sherri Ly in an e-mailed statement. “We look forward to meeting with FTA regarding certain points of clarification and submitting our comprehensive plan of action within 60 days or early September as requested. We have already begun taking action on nearly half of the FTA recommendations.”

The 116-page report was released June 17, and Metro had 30 days to submit initial responses to the document. A corrective action plan, in which the transit authority will outline how it will address the concerns raised by federal officials is expected to be submitted in September.

“Per FTA Safety Directive 15-1, WMATA had an initial 30-day period to provide additional information for consideration or to offer equivalent alternate actions,” said FTA spokesman Steve Kulm in an e-mailed statement. “The 30-day period expires today, July 17.  WMATA submitted a draft response on July 13 which FTA is now reviewing. FTA will be meeting with WMATA in the near future to discuss their draft document and to provide guidance as WMATA develops a detailed corrective action plan due in mid-September.”

Kulm said that because the document is in draft form, it will not be released publicly.

Using new authority given to them in 2012 by Congress, FTA officials initiated the unprecedented 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. Carol Glover, a grandmother from Alexandria, died, and more than 80 riders were sickened.

The report painted a troubling picture of WMATA, saying while it has made some gains, it has failed to follow through on efforts to improve safety since the 2009 Red Line crash that killed nine people.

Officials found that 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. Also troubling: staff members lacked adequate training and have no formal checklists to help guide them in doing their jobs. Employees frequently ignored rules, officials said, noting that several employees were seen using cellphones while working. In other instances, because of miscommunication between controllers and train operators, rail cars were directed into areas that should have been off-limits.

“These are serious findings that strongly indicate that, despite gains made since the Fort Totten accident, WMATA’s safety program is inadequate,” U.S. Secretary of Transportation Anthony Foxx said when the report was released. Acting FTA Administrator Therese W. McMillan called her agency’s findings an “important wake-up call” for WMATA.