The uncertainty over the fare increase highlights the growing dysfunction at the authority, which has increasingly been subject to the whims of Mr. Cuomo and his allies. For years, subway leaders had been planning to close the L train tunnel between Manhattan and Brooklyn to repair damage from Hurricane Sandy. Then Mr. Cuomo abruptly called off the shutdown this month.

Mr. Cuomo, a Democrat in his third term, has criticized the agency, complaining of its stodgy bureaucracy and saying he wants to “blow up the M.T.A.” The idea of calling off the fare increase — something Mr. Cuomo has supported for months — sounds good in theory. The subway is still far from reliable nearly two years after the system descended into crisis.

But the transit agency’s financial plan relies on modest fare and toll increases, every two years, across its sprawling system of subways, buses, commuter railroads and paratransit service. The fare increase is expected to bring in an additional $316 million per year.

The authority is working to make reforms and improve service with its existing resources, said Shams Tarek, a spokesman for the authority.

“The M.T.A. board will have robust discussion and decide on the best course of action in the context of the M.T.A.’s dire financial position, which requires fare and toll increases as well as new, sustainable, adequate sources of funding in order to balance the budget while avoiding painful service cuts,” Mr. Tarek said in a statement.

The authority’s board has been considering two options for fare increases of about 4 percent: The first would keep the base fare at $2.75, but end the bonus for buying a pay-per-ride MetroCard; the second would increase the base fare to $3 and double the bonus to 10 percent. A weekly pass would rise to $33, up from $32. A monthly pass could increase to $127, up from $121.

Even with the fare increase, subway leaders say the system is in a grim financial situation. They have warned that without new revenue sources, their only options would be even higher fare increases or drastic cuts to subway and bus service. The agency expects to have a deficit of nearly $1 billion by 2022.