On Wednesday afternoon, New York governor Andrew Cuomo announced "limited" service would resume on Thursday, four days after it was suspended as Sandy bore down on the east coast.

He said three of seven subway tunnels under the East River that were flooded by the storm had been cleared.

But he warned that the system, which carries over five million people a day, would not operate south of Manhattan's 34th street "because there is no power for that service."

Hopes of a quick return to normality had been dashed by images of flood water streaming into the system as Sandy hit.

"We've had floods in the past, but of course, never anything of this magnitude," authority spokesman Charles Seaton told AFP.

He said crews were working across the system to pump out the millions of gallons of water that cascaded into tunnels and stations at the peak of the so-called superstorm on Monday night.

He described extensive damage at many of the system's 468 stations.

"On the outdoor lines we're seeing downed trees, canopies blown off on the elevator stations, wind damage," he said. "There is water damage to stations in lower Manhattan and a lot of mud and debris on the tracks."

"In a couple of the under-river tubes, we had water up to the ceiling and water that stretched anywhere from 600 to a thousand feet."

MTA regularly pumps around 13 million gallons a day out of the system, because of rain or other water inflows, Seaton said.

But crews are now dealing with "many times the multiple of that."

The South Ferry station on the southern tip of Manhattan, right by the waters of the East River, was among those worst affected.

Video and pictures distributed by the MTA showed much of the station under water, the silver ticket turnstiles reflected in the murky lake -- dotted with debris including neon orange barriers -- now covering the station floor.

Ahead of the storm, the MTA sandbagged station entrances, covered street level grates and moved trains to higher elevations, protecting them from damage. They also cut power to the system in a bid to minimize damage.

"We took power off of the third rail because generally you're going to have more damage if water hits the equipment when its running," Seaton said.

It remained unclear how long it would take for subway service, which connects New York's five boroughs, to return to normal.

"There's no estimate on it at all," Seaton said.

"This is the most significant damage we've ever seen," he added. "I would ask New Yorkers to be patient."

And the cost of the damage done to the system is also unclear so far.

A 2011 Federal Transit Administration report on the likely effects of a "100-year storm surge" estimated costs could run up to $58 billion dollars.

"Direct physical damage alone was estimated at $10 billion," it said.

It warned that equipment in tunnels could be damaged "and would need to be disassembled, cleaned, and repaired or replaced to avoid corrosion and irreparable long-term damage."

And it said researchers estimated "a minimum recovery time of three to four weeks to reach 90 percent capacity."

In Midtown, New Yorkers waited for buses, which are free of charge for now.

"It's like World War Three over here!" laughed Regina Glick, a real estate broker waiting across the street. "It feels like we're disconnected from the rest of the world."