The metro-area mass transit system that moves millions of riders per day was crippled by massive flooding when Sandy swept through the area, and service is likely to be out for several days, officials said.

MTA Chairman Joseph Lhota said seven subway tunnels under the East River all had flooding, along with rail yards and bus depots. The 108-year-old subway system has never faced such devastation, he said.

Lhota told NBC 4 New York that he couldn't even begin to say when subways and commuter rails might be up and running. All the damage, he said, was to tracks, stations and tunnels; subway cars and buses were not harmed.

"It's like nothing we've ever experienced before," he said. "We are in the assessment stage."

But Bloomberg estimated it would be four or five days before subway service is restored. Officials said limited bus service would resume Tuesday, with fares waived.

Lhota said buses would be used to replace subway service along lines where repairs are expected to take longer.

The MTA cut power to some subway tunnels in lower Manhattan, after water came into the stations and tracks. The South Ferry station was flooded up to the ceiling, said Lhota.

The Metro-North Railroad lost power from 59th Street to Croton-Harmon on the Hudson Line and to New Haven on the New Haven line. The Long Island Rail Road evacuated its West Side Yards and suffered flooding in one East River tunnel.

Lhota said the Hugh Carey Tunnel, formerly known as the Brooklyn-Battery Tunnel, and the Queens Midtown Tunnel also took on water. Each tube of the Hugh Carey Tunnel was filled with 43 million gallons of water.

Flooding was also reported in PATH train stations in Hoboken and Jersey City along the Hudson River.

A surveillance camera inside the underground station in Hoboken captured water gushing in through an elevator door.

PATH officials say flooding has also occurred at the underground station at Exchange Place in Jersey City. They are not able to say how bad the flooding is.

PATH service between Manhattan and New Jersey has been suspended since midnight Sunday, and will remain suspended "indefinitely," officials said Tuesday.