Gov. Andrew M. Cuomo is calling on the MTA to have a forensic auditor comb over its proposed $51.5 billion infrastructure spending plan to address “skepticism” about the agency’s ability to pull it off.

In a letter sent Monday to Metropolitan Transportation Authority chairman Patrick Foye, the MTA Board and MTA inspector general, Cuomo directed that an ongoing forensic audit of the agency’s finances be expanded to include the MTA Capital Program, which aims to fund major transportation infrastructure projects through 2024, including at the Long Island Rail Road.

“There is much skepticism surrounding the MTA's ability to purchase, construct, repair or administer efficiently,” Cuomo wrote. “We do not want that skepticism to become an obstacle to the necessary investments and improvements the Capital Plan provides for the commuters of New York.”

A forensic audit of the embattled transit agency’s finances was among several reforms adopted by the State Legislature this year as a condition for lawmakers' approval of a congestion pricing plan that is expected to generate about $1 billion in toll revenue for the Capital Program, which was unanimously approved by the MTA Board last month. Final approval of the plan rests with the state's four-member Capital Program Review Board.

In a statement Monday, MTA spokeswoman Abbey Collins said the authority understands that "the Governor, Mayor, Legislature and City Council want fiscal integrity from the MTA."

"They have all made that clear," Collins said. "And we believe the forensic audit will provide that additional confidence.”

The MTA is relying heavily on the state and New York City to fund the Capital Program, which allots $5.7 billion to the LIRR, including for 160 new trains, the replacement of about a third of track switches, and for new signals on the LIRR’s Montauk and Port Jefferson lines. The MTA plans to use revenue generated from the state, including congestion pricing tolls and a mansion tax, to back about $25 billion in new bonds, and is counting on another $3 billion each from the state and city.

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At an MTA Board meeting in September, Foye said he expected the audit would “look historically” at the MTA’s past spending practices, including for potential waste, fraud and abuse, and to make sure it is following best practices in the transportation industry.

“The forensic auditors are doing their thing. They’re independent,” Foye said. “My focus with the forensic auditors right now is to work with them to accelerate some of their work product that they’re doing to be able to inform all stakeholders and decision makers.”

In his letter, Cuomo said the audit must go beyond “mere accounting.”

“Please instruct the auditor to review the Capital Plan, and the MTA's past performance, to identify costs that are beyond market norms or comparable costs in the private sector,” Cuomo wrote. “New Yorkers should invest in the MTA, but they have a right to demand management competence.”

As one example, Cuomo cited the MTA’s proposed cost for installing new elevators at a single subway station at $82 million. “That estimate strains credulity,” he said.

Sen. James Gaughran (D-Huntington), who pushed for the MTA forensic audit to be included in the state budget, on Monday applauded Cuomo for "speaking so loudly on this issue."

"We want to make it very clear that this is a top priority," said Gaughran, who added that the audit aims at "making sure we're not wasting any money, and that we’re getting as much for the commuters as we possibly can as we move forward.”

In his letter, Cuomo also said the audit should review purchases of equipment and material in order to provide "a basis to feel confident that the funding will be well spent." He also called for MTA Inspector General Carolyn Pokorny to review the "integrity" of the MTA's procurement and inventory control systems.

Pokorny's office did not immediately respond to a request for comment.