The assault on the MTA’s already battered finances could now come from yet another front: the federal government. The new Republican majority in the House of Representatives passed a rule Wednesday that would allow reductions in federal transportation spending, including investment in transit. That puts previously secure federal funds on the negotiating table, making it that much harder for the MTA to balance its books.

For more information about the Republican rule, check out Tanya’s report over at Streetsblog Capitol Hill. As she explained, Congress no longer has to spend a set amount annually from the Highway Trust Fund (which, despite the name, is really a pot for surface transportation, including transit and bike-ped projects). Instead of spending being guaranteed, Congress can just hang onto the money.

That rule drew opposition from a wide-ranging coalition, including traditional highway boosters like the U.S. Chamber of Commerce. One group that’s particularly anxious, however, is the MTA. The potential loss of some federal funding — and the uncertainty over how much might get cut — is more bad news for New York transit.

Transportation Nation’s Kate Hinds reported yesterday that MTA Chair Jay Walder had sent a letter to Rep. Anthony Weiner, pleading against the new rule, before it passed in a straight party-line vote. The MTA’s “five-year capital program depends on steady, predictable multi-year funding,” Walder wrote. “If transportation funding is subject to the vagaries of the appropriations process, transit projects that generate jobs and economic activity throughout New York State will be at risk.” Streetsblog has a request in with the MTA to find out how the rule change might affect ongoing capital projects like the Second Avenue Subway.

As things currently stand, the MTA’s budget already doesn’t add up. There’s a $10 billion gap in its five-year capital program, and Governor Cuomo and the state legislature have no plan to fill it. The potential loss in federal funds could add to that deficit. Then throw in the distinct possibility of Albany stealing more dedicated funds from the MTA to close its own multi-billion deficit — with the state budget worse than ever, those raids could be even larger than before. There’s even the chance that the newly-empowered Senate Republicans will win their fight against the payroll mobility tax, which could yank hundreds of millions of dollars away from transit riders each year.

With the new House rules, there seem to be far more ways for the MTA to lose money looming over the horizon than hopes for it to get back on its feet.