New Jersey Transit faces a widening examination of its safety practices after federal regulators discovered hundreds of potential work-hour violations, including altered duty logs and shifts longer than permitted.

Federal Railroad Administration inspectors recommended penalties in September after they found timekeeping irregularities by a small sample of engineers and other on-board crew, according to material obtained by Bloomberg in response to a public-records request.

The lapses, the inspectors wrote, allowed employees “to work longer or more preferred jobs” at the nation’s third-largest mass-transit operator, a crucial link to New York City employment. The broadening review comes as lawmakers question safety and finances at an agency that in the 1990s was a model for innovation and service, only to suffer increased breakdowns and more crowded rush hours as the state provided less budget aid.

“Hours-of-service laws are not foolish,” Martin Robins, New Jersey Transit’s deputy executive director when the agency was founded in 1979, said in an interview. “They’re set up for a reason: to protect the public.”

The reports are key to combating fatigue, a factor in deadly train wrecks in recent years in Connecticut, Arkansas and Iowa. In response to a fatal New Jersey Transit crash and a Long Island Rail Road wreck in Brooklyn that injured more than 100 people, five U.S. senators this month urged the National Transportation Safety Board to review railroads’ testing procedures among engineers for sleep disorders.

In the matter of New Jersey Transit’s duty logs, inspectors reviewed two days of handwritten records in June, and alleged 246 instances of improper documentation, including alterations to 42 signed records and 34 instances of insufficient rest time between shifts.

Nancy Snyder, an agency spokeswoman, said most lapses were “record-keeping clerical issues,” and that the agency is considering switching to an electronic system to avoid such errors.

“New Jersey Transit routinely reviews employees’ hours of service to ensure they are in compliance with federal regulations,” Snyder wrote in an e-mail. “Trains are not routinely staffed by individuals working hours beyond what regulations allow.”

Still, disciplinary action has been taken against one employee and proceedings are pending against 35 others, Snyder said. Now, while regulators consider whether to seek penalties against the railroad, federal examiners are looking for widespread discrepancies among handwritten logs submitted daily by New Jersey Transit’s 1,600 engineers and other on-board crew.

The Railroad Administration’s “audit and our enforcement actions remain ongoing,” Matthew Lehner, a spokesman for the U.S. Transportation Department, said in an e-mail. No hours-of-service violation notices have been issued.

The New Jersey Transit workers whose duty logs raised red flags are among the train personnel nationwide at greatest risk of fatigue and most likely to exceed monthly work-hour limits, according to a 2013 report by the Federal Railroad Administration. Sleep disorders, including apnea, also appear to occur at a higher rate among railroad employees than other U.S. workers, the report found.

Earlier research by the federal agency found that crew tiredness had a role in about 25 percent of train accidents attributed to so-called human factors, such as inattentiveness and poor judgment.

New Jersey Transit, with 90 million passengers annually, has been beset in recent years by crowding, more frequent breakdowns and unreliable service. Rail service Tuesday was returning to normal a day after a wind-driven storm took down electrical wires along tracks in Linden, suspending New Jersey Transit and Amtrak trains for hours along the Northeast Corridor, the nation’s busiest line.

Snyder said the railroad is cooperating with the expanded Railroad Administration inquiry, which began in June.

A separate review of operations and finances is under way by New Jersey lawmakers in response to a September wreck in Hoboken that killed a woman on a platform and injured more than 100 passengers. The train’s engineer had undiagnosed sleep apnea, his lawyer has said.

At a hearing in Trenton in November, Steve Santoro, the agency’s new executive director, said lack of funding is at the root of many of New Jersey Transit’s troubles.

From 1990 through fiscal 2017, New Jersey Transit used 7.1 billion intended for capital improvements to cover day-to-day expenses. Forty-two percent of those diversions took place under Gov. Chris Christie, R.

From January 2011 through July 2016, New Jersey Transit logged the most train accidents and the highest safety-violation fines of any U.S. commuter railroad, federal data show.

At the November hearing, Santoro hearing disclosed instances of forbidden cellular-phone use, locomotives left unattended and missing emergency equipment, all documented by federal inspectors. In response, he said, the railroad was stepping up enforcement and expanding training. He also committed to fully staffing a safety office that was operating without a deputy chief and about a dozen others.

In some cases, the records were missing documented days off or such details as travel time to assignments, which counts toward maximum hours. Each penalty carries a fine of as much as $25,000, though those amounts typically are negotiated down.

Assemblyman John McKeon, 58, D, who is co-leading the legislative inquiry, said the Railroad Administration’s findings on duty logs, if proven, are “intolerable to the thousands of people who rely on New Jersey Transit every day.”

“Whether mismanagement or lack of personnel or outright violating of federal safety rules, the FRA being involved, with all its heft, can only help,” he said in an interview.

(c) 2017, Bloomberg · Elise Young