The latest deficits were caused in part by declining ridership, which has led to lower revenue projections, officials said. The decline is worrisome because it is happening as the city’s population is increasing and tourism is booming.

Officials blamed the drop on competition from Uber and other ride-hail apps, and on night and weekend closings for construction work that are needed to fix the system. Some riders, fed up with constant delays, have simply abandoned the subway.

The authority’s board is considering two options for fare increases of about 4 percent in March: 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.

At the same time, tolls on M.T.A. bridges and tunnels could increase by 8 percent for E-ZPass users. At the Verrazzano-Narrows Bridge — already one of the country’s most expensive crossings — where tolls are collected only when entering Staten Island, the E-ZPass toll could rise to $12.44, up from $11.52, and the toll via mail could increase to $19, up from $17.

The board will vote in January about whether to raise fares and tolls in March and by how much. Some transit advocates have said the fare increase should be canceled because service is so unreliable. They are urging Mr. Cuomo to instead pass a comprehensive transit funding plan in Albany with congestion pricing at its core.

“Riders have been paying more every two years for almost a decade,” said John Raskin, executive director of the Riders Alliance, an advocacy group. “But in that time, public transit service has deteriorated.”

Mr. Lhota returned to the authority last year to help fix the failing subway. But he soon faced questions over potential conflicts of interest and outside jobs.