BOSTON — The Boston-area’s aging subway system has for years neglected safety and maintenance while it focused on long-term capital projects, federal transportation officials said in a highly critical report based on a review earlier this year in response to several accidents and other problems with the system.

The Massachusetts Bay Transportation Authority “is not effectively balancing safety-critical operations and maintenance activities with its efforts to deliver capital projects,” the Federal Transit Administration’s report said. “This lack of balance is at the center of many of the MBTA’s safety challenges.”

“The system has to get safer. It’s just not an option,” Paul Kincaid, the FTA’s associate administrator for communications and congressional affairs, said in an online news conference.

While the capital budget has quadrupled in four years, funding cuts to the operations and maintenance budget have resulted in a reduction in hundreds of millions of dollars and hundreds of positions.

“The combination of overworked staff and aging assets has resulted in the organization being overwhelmed, chronic fatigue for key positions in the agency, lack of resources for training and supervision, and leadership priorities that emphasize meeting capital project demands above passenger operations, preventive maintenance, and even safety,” the report said.

The FTA’s report includes four “special directives,” requiring 53 separate actions that the transportation authority must take, including addressing worker shortages, prioritization of safety management, safety communication, and operating conditions, policies, procedures, and training.

The authority, which hundreds of thousands of people rely on every day to get to work, medical appointments, and reach the city’s top tourist attractions, is committed to working with the FTA and has already started addressing some of the directives, General Manager Steve Poftak said in a separate Wednesday news conference.

“We have been given a series of special directives by the FTA and a series of findings that will allow us to improve how we operate as an organization,” he said.

The transportation authority has completely shutdown of the Orange Line for 30 days to complete maintenance work that would otherwise take five years.

The agency also established a Quality, Compliance, and Oversight Office to formulate and implement actions to address the report’s findings and will “focus on assessing, recruiting, and hiring as part of workforce management, collecting and analyzing safety data, instilling safety culture across the organization, and improving operating practices,” it said in a statement. The office will report directly to Poftak.

An $840 million supplemental budget proposal filed by Gov. Charlie Baker Wednesday included $200 million for the MBTA to address the FTA’s directives and another $10 million to help recruit and train staff.

“I appreciate the FTA’s thorough review of the MBTA, and this report will make the system safer and more reliable for riders and the T workforce,” the Republican governor, who promised improvements as far back 2015 after a severe winter paralyzed the system, said in a statement.

Poftak and Kincaid said there are no overnight fixes and the process could take years.

“We want today to be the beginning of rebuilding the infrastructure, the culture, and critically the trust around an important community asset that the people of Massachusetts support with their tax dollars and their ridership,” Kincaid said during an online news conference.

There shouldn’t have to be a “false choice” between capital expenditures and operations funding, said Josh Ostroff, interim director of Transportation for Massachusetts, a public transit advocacy coalition.

“We urge our partners in state government to maintain the focus on capital investment, which is urgent and overdue, but not at the expense of rider safety and public confidence,” he said in a statement.

The report also criticized the state’s Department of Public Utilities, which is responsible for safety oversight, saying “the DPU has not consistently required or enforced timely assessment and mitigation of safety risk for passenger operations to prevent organizational blindness to emerging safety concerns.”

The report is specific to the subway system and not commuter rail or bus networks.