New York's Medicaid program is on track for a $2.9 billion shortfall, potentially complicating next year's state budget. 

The shortfall is projected as the program has already spent more than 60 percent of its state-funded budget by the end of September, about $13.1 billion, based on a cash report released this week by Comptroller Tom DiNapoli's office. ​

Gov. Andrew Cuomo’s administration had sought to delay $1.7 billion in Medicaid into the 2019-20 fiscal year — a move that doubled spending in April.

As Bill Hammond of the Empire Center think tank pointed out on Monday, this move was meant to avoid payment cuts that would have been triggered under the “global cap” for the program.

“This maneuver was not disclosed to the public until May – after the current budget was adopted by lawmakers – and did not become widely known until July,” he wrote in a post. “Since then, the governor’s aides have confirmed that spending continues to exceed expectations – and warned that cuts or further payments delays may be necessary in the near future.”

The Division of Budget, an arm of the Cuomo administration, noted costs have increased under the Medicaid program, and blamed the federal government in part, among other factors.

“State spending on Medicaid has been rising as we reimburse providers for a higher minimum wage, expand enrollment to drive the number of uninsured New Yorkers to record lows — an effort now strained by declining Federal support — and long-term managed care costs grow due to our aging population,” the budget office said.

“We have said that Medicaid spending is trending above the Medicaid Global Cap established by this administration in 2012 and we will present a plan as part of the Executive Budget in January that will fix the structural imbalance while also continuing high-quality care for more than six million New Yorkers.”