Nine of the city's 14 underwater tunnels were damaged by flooding, and necessary repairs could force closures for years to come.
The worst hit tunnels, on the R and G lines, are currently under repair.
Other tunnels, particularly in lower Manhattan, will also face shutdowns in the future to fix salt water contamination and corroded equipment.
Additionally this year, MTA Chairman Thomas Prendergast says that tunnels flooded in lower Manhattan are subject to closure at night and on weekends for repairs.
Work already is under way at the flooded Montague and Greenpoint tubes.
Prendergast spoke at a breakfast of the nonpartisan Citizens Budget Commission on Tuesday.