An MTA contractor working on the Second Avenue Subway caused a water main break on the East Side today, flooding the basement of a nearby hospital, the city said.

Skanska, a construction firm working on the long-delayed subway tunnel, hit the 12-inch pipe near 66 Street and Second Avenue, said Mercedes Padilla, a spokeswoman for the city Department of Environmental Protection.

Water then flowed into the mechanical room of Sloan-Kettering Cancer Center, she said.

The water has already been cleared, and service hasn’t been cut off to any residences, she said.

Workers were using machinery to remove water from underneath the sidewalk this afternoon.

Skanska will be making the necessary repairs, Padilla said.