The Metropolitan Transportation Authority forecasts a half-billion dollar shortfall from the current budget plan.
The MTA said only about half of commuters have returned to their pre-pandemic commutes on buses, trains and subways.
New York State Comptroller Thomas DiNapoli said hopes of a quick recovery from the multi-billion-dollar loss seem to be fading, as COVID-19 variants continue to spread.
He said if commuters continue to work from home three to four days a week, MTA income will be $500 million less than forecast.
The federal government gave the MTA $15 billion in aid. That money is predicted to run out by the end of 2025.