What does it look like when mild-mannered accountants hit the panic button? Something like the latest report on MTA finances from State Comptroller Tom DiNapoli’s office [PDF]. According to the comptroller, the MTA is entering a financial situation unprecedented since the agency’s first capital plan in 1982.

In 2009, the transit agency put forward its most recent five-year capital program, which pays for critical repairs and system expansions. At the time, the state government only funded the first two years of that plan, leaving a $9.9 billion deficit. Last July, Governor Andrew Cuomo decided he didn’t need to provide the rest of the funding. Unwilling to allow the transit system to collapse again or to give up on half-complete projects like the Second Avenue Subway, the MTA had no option but to pay for the rest of capital plan on credit.

That brings the MTA’s total borrowing for the five-year period to a total of $14.8 billion, according to the comptroller, the largest amount the MTA has borrowed in its history. More than 60 percent of the entire capital plan is being paid for with debt. Any debt incurred to pay for the 2015 capital plan would only be on top that total.

Since George Pataki first decided not to pay for the capital plan, the debt he incurred has been wreaking havoc on the agency’s finances. According to the comptroller, Cuomo’s legacy will be similar. “Such a heavy reliance on debt would place a huge burden on the operating budget,” he writes, “just as heavy borrowing in the past has contributed to the MTA’s current problems.”

That level of debt means that even the fare increases already scheduled to take place every other year won’t be enough to keep the agency in the black. Warns the comptroller, “Even if the MTA raises fares and tolls by 7.5 percent in 2013 and 2015 as it already plans, and raises them by the same amount in 2017, it could still face budget gaps that would grow from $600 million in 2016 to $1.2 billion by 2018.” Last year’s unprecedented service cuts only saved $93 million.

And the real news could be worse than that. The comptroller is analyzing the MTA’s current budget plans, but those plans are built on extremely optimistic assumptions. Those already enormous deficits would soar even higher if the MTA doesn’t force a wage freeze on TWU members, if the city doesn’t chip in extra revenues from the area around the Second Avenue Subway, or if Republicans in Congress cut federal transit funding, just to name a few possibilities.

DiNapoli also warns of additional state raids on dedicated funds. “The MTA also needs to be prepared if New York State enacts another round of budget cuts to balance its budget. In each of the last two fiscal years, the State has reduced planned funding for mass transit.” If any of these scenarios come to pass, the MTA deficits will be even higher.

Without new revenue, transit riders are looking at enormous fare hikes for the foreseeable future. Albany knows it. The only question is whether lawmakers are going to do anything about it.