New Jersey’s financial support for NJ Transit is getting fresh scrutiny following the deadly Sept. 29 crash of a commuter train at the Hoboken terminal.

For years, NJ Transit officials appealed for more money from the administration of Gov. Chris Christie, said people familiar with the conversations, concerned the agency’s strained finances could lead to safety and operational problems across the network. ​

Meanwhile, Mr. Christie, a Republican, and the state Legislature, which is led by Democrats, have sent NJ Transit a dwindling subsidy from the state budget over the past five years. This transit-specific subsidy, known as operating assistance, has fallen from some $285 million in 2012 to $33 million in 2016. In 2005, the subsidy from the budget stood at about $278 million, according to the state’s Department of the Treasury.

As the subsidy has fallen, Trenton and NJ Transit have found other ways to pay for operations, largely by diverting money from other state financial pools, such as the New Jersey Turnpike Authority and a state clean energy fund. In 2015, NJ Transit also raised fares 9%, with Mr. Christie’s blessing, the second fare hike since Mr. Christie took office in 2010.

Critics question some of those budgeting strategies—either they draw on money intended for something else or on sources of money that aren’t necessarily recurring year-to-year. They charge that the declining subsidy reflects a weak commitment by Mr. Christie to the transit system even as the system’s ridership has steadily climbed in recent years.