New Jersey Transit workers lay down pallets and boards for commuters to walk on in a flooded hallway near the site of last week’s train crash in Hoboken, N.J. (Julio Cortez/AP)

The New Jersey transit agency involved in a rail station crash that killed one person and injured more than 100 last week already was under scrutiny by federal authorities after dozens of safety violations were uncovered this summer.

The Federal Railroad Administration discovered the violations after conducting an extensive audit of New Jersey Transit’s commuter rail operations, said an individual who was familiar with the audit but who was not authorized to comment publicly.

The cause of Thursday’s crash, in which a train barreled into the Hoboken, N.J., station, is under investigation by the National Transportation Safety Board and the FRA. The train, which was being pushed by a locomotive, crashed over a barrier, killing a woman on the platform who was struck by debris.

The FRA declined to comment on its earlier investigation into the transit agency. The scrutiny on the agency was first reported by the Wall Street Journal and then independently confirmed by The Washington Post.

The FRA, concerned about a leadership vacuum and an increase in safety violations, began to review New Jersey Transit’s commuter rail operations in June. Several FRA inspectors found dozens of safety violations, informing the transit agency of their findings.

The violations were described as “operational,” meaning they had to do with the way trains were operated rather than with physical problems such as infrastructure.

Before the Hoboken crash, the FRA was taking steps that would have forced compliance with safety regulations, the individual familiar with the audit said.

New Jersey Transit is the nation’s third-busiest commuter system, serving many of the people who live in northern New Jersey and work in New York City.

Like many transit agencies, New Jersey Transit has been financially squeezed and has had many veterans depart from leadership positions, including its executive director, Veronique Hakim, who resigned last year to join the Metropolitan Transportation Authority in New York.

The man selected to fill Hakim’s position turned down the job, leaving New Jersey Transit in the hands of an interim director.

The agency also is dealing with a $45 million budget gap.

New Jersey Transit has also faced scrutiny over its bus operations. In August, two buses collided in Newark, resulting in the deaths of one driver and a passenger.

Last week, two New Jersey Transit buses bound for Manhattan collided in the Lincoln Tunnel connecting New York and New Jersey, injuring dozens of passengers.

Some federal officials said the Hoboken crash could have been prevented if the transit agency had installed a device known as positive train control. The system would have slowed the train before it entered the station where it crashed. Some witnesses said the train was traveling at a high speed when it entered the station.

According to the latest FRA accounting, New Jersey Transit has not installed the system in any of its 440 engines or put in place the 124 rail-side towers that would be needed to communicate with the trains.

NTSB officials said Sunday they are having trouble determining the speed of the train at the crash because the recovered event recorder was not working at the time. In addition, the engineer, Thomas Gallagher, 48, has no memory of the crash.

The recovered “black box,” which would have contained speed and braking information critical to the investigation, was an older model built in 1995, NTSB vice chairman Bella Dinh-Zarr said at a news conference Sunday. Engineers are hopeful they can recover the train’s other event recorder — likely a newer model — which is still in the leading car. Investigators have been unable to access the car because it is buried in debris from the crash, and contractors are still working to remove it.

Faiz Siddiqui contributed to this report.