Even before one of its trains crashed in Hoboken Terminal on Thursday morning, killing one woman and injuring more than 100 others, New Jersey Transit was an agency in distress.

The third-busiest commuter system in the country, New Jersey Transit has been operating without an executive director for nearly a year, its board of directors has not met for three months and it has not explained how it will close a $45 million gap in its budget this year. Last month, two of its buses collided in downtown Newark, leaving two people dead.

The cause of the fatal train crash has not been determined. But whether it proves to have been a case of human error or of mechanical failure, it is sure to focus more attention on a transit agency that has been operating in secrecy.

New Jersey Transit’s management “has been told to go into a bear cave and disappear until told to come back out,” said Martin E. Robins, a former deputy executive director of the agency. “We don’t know anything about what’s going on.”

Mr. Robins, who has been a critic of the agency in recent years, said he could not recall its board suspending monthly public meetings before this year. It has done so since June, when New Jersey Transit’s interim management grappled with a state budget that left the agency about $45 million short of what it needed to operate this year.

Since then, Gov. Chris Christie and legislative leaders have failed to reach an agreement on an increase in New Jersey’s gas tax that would have replenished the state’s Transportation Trust Fund. That fund, which nearly ran dry this summer, provided more than one-fifth of New Jersey Transit’s annual budget. In July, Mr. Christie ordered the suspension of all highway and transit projects paid for by the trust fund.

Mr. Robins and other transit advocates warned that cutting off financing for so many improvements could lead to more mechanical and safety problems.

“It does beg the question how quickly and how severely is the transit infrastructure in New Jersey failing, given the inadequate funding and resources that they’re being given,” said Veronica Vanterpool, executive director of the Tri-State Transportation Campaign. “The public has a right to know what the budget numbers are, how is N.J. Transit staying afloat these days? How are they covering their day-to-day operating costs?”

Mr. Robins pointed to the sharp reduction in the annual contribution to New Jersey Transit from the state’s general fund, less than $35 million last year — about one-tenth of what it was in 2009.

“This is not an incompetent agency,” Mr. Robins said in an interview earlier in the week. “What you’re dealing with is an agency that’s being systematically starved.”

And since November, it has been an agency without an established leader.

Veronique Hakim, who was highly regarded as the executive director, resigned to join the Metropolitan Transportation Authority in New York. After a search for a successor, New Jersey Transit held a special meeting in April to appoint William Crosbie. But Mr. Crosbie turned down the job, leaving Dennis Martin the interim director for an indefinite period.

“Right now, there’s a leadership vacuum at the agency,” Ms. Vanterpool said.

While its management and funding have been in flux, New Jersey Transit had not been plagued by safety issues heading into this summer. But that changed dramatically on the morning of Aug. 19, when a bus carrying passengers in downtown Newark crossed the path of an empty bus. The collision sliced one bus in half and killed one of the drivers. A passenger died later from her injuries.

On Monday morning, two New Jersey Transit buses collided in the Lincoln Tunnel, injuring dozens of passengers and causing long delays for other commuters trying to get into Manhattan.

But according to federal records, the last New Jersey Transit rail accident that resulted in the death of a passenger happened 20 years ago. On a February morning in 1996, a Hoboken-bound train overshot a stopping point and ran into the path of another New Jersey Transit train. The engineers of both trains and one passenger were killed, and more than 160 others were injured.

Rail-safety advocates argue that crashes like that one could be prevented by a technology known as positive train control, which automatically brakes a train that has run a stop signal or exceeded speed limits. Federal officials have called for passenger railroads to adopt positive train control by the end of 2018.

In its 2015 annual report, New Jersey Transit said that it had equipped a locomotive and a cab car with the components needed for the system and that it would start installing hardware along tracks this year “when design plans are finalized.” The Federal Railroad Administration said that New Jersey Transit had not yet installed the technology.

It was not clear on Thursday whether the system could have prevented the crash in Hoboken.

At a news conference, Mr. Christie, a Republican, and Gov. Andrew M. Cuomo of New York, a Democrat, were reluctant to address that question. Mr. Christie said officials first had to determine the cause before deciding what steps should be taken in the future. “We cannot answer whether any other apparatus or system could have prevented it,” Mr. Christie said.

Mr. Cuomo said that the technology could help in some circumstances, but that officials did not yet know why the train was traveling at a high speed.

Hundreds of people die on the nation’s rails each year, but the vast majority of them are motorists or pedestrians who get in the paths of trains and are struck. Workplace accidents kill railroad workers far less often, but still fairly regularly.

Passenger fatalities are much rarer, about seven for every 100 million miles traveled by passenger trains. But there have been some major, recent exceptions.

Last year, six people died, including five passengers, when a Metro-North Railroad train hit an S.U.V. on the tracks — the worst accident in the railroad’s history. Three months later, an Amtrak train derailed while going too fast around a curve in Philadelphia, killing eight people.