Congestion Pricing Is at Risk. So Is the M.T.A.’s $68 Billion Plan.

The M.T.A. has a five-year capital budget proposal for critical upgrades to the subway, buses and commuter railroads. The catch: It depends on $14 billion in federal funding.

While federal officials are clashing with New York over congestion pricing, the tolling program that President Trump has vowed to kill, there is another transit fight underway between Albany and Washington.

The $68 billion capital plan, a five-year budget proposal that includes a slew of critical upgrades for the subway, buses and commuter railroads, is the biggest such request the Metropolitan Transportation Authority has ever made. The plan, which would run from 2025 to 2029, comes as the Trump administration is not only trying to kill the toll but is also threatening to defund an untold number of other transit priorities.

So far, the M.T.A. has identified funding for only about half of the plan and is expecting the federal government to contribute $14 billion, a sum that was optimistic even before its tolling dispute with Washington, budget analysts said.

The state is relying on congestion pricing to fund transit upgrades that were part of the last five-year capital plan, and its termination could throw the new budget into disarray, as overdue projects pile up. The capital plan is separate from the M.T.A.’s annual operating budget, which largely pays for expenses like worker salaries, energy expenses and some financing costs and is partly funded by fare revenue.

At stake is a long list of repairs and improvements to New York City’s aging transit system that, if put off any longer, could plunge New York into another “Summer of Hell” — the notorious series of power outages, track fires and delays in 2017 that infuriated riders — Janno Lieber, the head of the transit authority, said.

“We have to invest in the system to protect the riders,” Mr. Lieber said in an interview Tuesday in Albany.