Transit workers moved trains from outdoor yards, parking them in tunnels around the city to protect them from the up to 12 inches of rain forecast for the city, The New York Times reported.
Mayor Michael Bloomberg said the subway system was unlikely to return to service Monday.
"Plan on a commute without mass transit on Monday morning," he said.
City officials said high tide at 8 a.m. Sunday would pose a significant flooding threat as Irene lingers along the Eastern Seaboard.
"That is when you'll see the water come over the side," Bloomberg said at a news briefing Saturday. He said only 1,400 people had arrived by 3:30 p.m. at 91 emergency centers prepared to handle up to 70,000 people.
Bloomberg said a 66-year-old man was injured when he fell from a ladder as he tried to cover the windows of his Queens home and was in serious condition at Jamaica Hospital.
New York Gov. Andrew Cuomo called in 2,000 National Guard troops to help police, the Metropolitan Transportation Authority and the Port Authority of New York and New Jersey cope with the storm and its aftermath.
New Jersey Gov. Chris Christie said more than a million people were evacuated in the southern part of the state, and 1,500 National Guard troops were deployed.