The state budget, recently finalized after prolonged negotiations, puts Gov. Andrew Cuomo’s commitment to the MTA in question, transit advocates charged Tuesday.

Cuomo’s budget has allocated $4.486 billion toward the MTA, a $30 million increase from last year. It also includes a $65 million cut of MTA funding from the state’s general fund — a sticking point that the advocates have battled the administration on since February.

In the final budget, as suggested by the Assembly, the $65 million was restored — but in the form of capital funding, not for the day-to-day operational aches of the subway system, which advocates fear will worsen.

“Public transit is a mess, and it’s the riders who suffer the consequences. Subway delays are common, buses are notoriously slow, and it’s increasingly hard to predict whether you’ll actually get to work on time in the morning,” said John Raskin, executive director of the Riders Alliance.

“The MTA needs a Marshall Plan of investment, billions of dollars to modernize the system, but instead we’re playing budget games and cutting money that riders thought we could rely on,” he continued. “This is no way for Gov. Cuomo to show leadership on improving public transportation.”

The $65 million in capital was somewhat of an empty gesture, according to Raskin’s group. After the payroll mobility tax, an important but politically challenging revenue source for the MTA, was scaled back during a restructuring in 2011, Gov. Cuomo pledged to make the agency whole through the state’s general fund. Without the $65 million restored through the general fund, MTA money could be in jeopardy in budgets to come.

A spokesman for Cuomo, Jon Weinstein, dismissed the notion, pointing to the fact that the state’s overall commitment to the budget has increased.

“Some people can never take yes for an answer — especially when they’re paid not to,” Weinstein said in a statement. “This budget provides the MTA record funding.”