While the agency said it would avoid major cuts in 2021 and 2022, it still faces an $8 billion deficit over the next four years and the possibility of cuts in the near future without additional federal aid.

“In the short and midterm there is significant relief, but we still have a long-term structural, fiscal problem that we have not dealt with” said Andrew Rein, the president of the Citizens Budget Commission, a financial watchdog. “The bottom line is we are not out of the woods, but we can see the light through the trees.”

Still hanging in the balance is the agency’s sweeping $54 billion plan to modernize the system, including replacing an antiquated signal system that is a major cause of delays and disruptions. That plan was suspended after the pandemic hit but parts of it will be revived this year, according to transit officials.

Making the system more reliable is a crucial step to luring back riders as New York struggles to recover from the financial crisis set off by the outbreak.

“The reality is they won’t have the money to do everything, so they need to prioritize state of good repair and critical replacements first,” Mr. Rein said.