NEW YORK -- New Jersey Transit train swept into the station, looking more like the subway than a commuter train. The seats were full. The vestibules were full. Even the aisles were full, so crowded that conductors could not move down them to collect tickets, reports the New York Times.

It was nothing out of the ordinary. Just another weekday morning in Newark, 8:26 a.m. And once again Simone McGowan, 34, a registered nurse, was throwing herself into the maw.

"I've been commuting into the city since I was 16," she said, joining the wide crowd squeezing through the narrow door. "But I don't know how much longer I can take this."

She is not the only one wondering. On many morning trains heading into Manhattan, the number of passengers has increased 44 percent over the last three months -- the kind of growth that officials thought would take a decade.

And if New Jersey Transit looks like the subway, the PATH system on many mornings can look and feel even worse. With its busiest station, at the World Trade Center, out for at least two years, and ridership still surprisingly high, four of the other five Manhattan stations -- at Christopher, Ninth, 14th and 33rd Streets -- are experiencing passenger loads roughly double what they were before Sept. 11.

"All of those stations are bursting at the seams right now," said Steve Coleman, a spokesman for the Port Authority of New York and New Jersey. "There's nowhere for people to go."

The statement is one that could be superimposed on dozens of transportation hubs around the city, and it describes a harsh, new reality: even as many things seem to have recovered remarkably since Sept. 11, the precariously balanced network of highways and rails, long overstrained before the attacks, is still suffering terribly and will continue to do so for much longer than most commuters had feared, transportation officials say.

Though the subway recovered fairly quickly after the attack, it is still snarled weekly by security-related shutdowns and delays that officials say will probably not go away soon. The same uncertainty reigns on the roads, where tunnels and bridges can be closed on a moment's notice.

"There's a new normal, and we can't go back," said John Kaehny, executive director of Transportation Alternatives, a pedestrian advocacy group that is part of a coalition of officials, advocates and business leaders trying to map out the future of transportation around the city.

At least for the foreseeable future, many of the problems will be the result of an unexpected conundrum -- commuters trying to switch from cars to mass transit, as officials have always urged. But riders are often finding the system too overburdened to handle them, especially as they make their way to Midtown, where thousands of jobs have moved from Lower Manhattan.

Traffic restrictions after the attack -- both security checkpoints and the morning ban on single-occupant vehicles at several crossings into the city -- have forced tens of thousands of drivers out of their cars and onto commuter trains and buses, several transit agencies say.

"We're pretty sure that many inveterate motorists have decided to give up their wheels for ours," said Dan Brucker, a spokesman for the Metro-North Railroad.

Both Metro-North and the Long Island Rail Road say their ridership into the city has remained level, or just below where it was before Sept. 11. But given that officials had expected a precipitous drop with the loss of so many jobs in Lower Manhattan, the numbers suggest that the railroads have actually picked up new riders.

Roads and bridges have been overcrowded for years, so the switch to transit is a phenomenon that urban planners had long hoped for and one that has already made morning car commuting into the city noticeably easier. But the switch was much larger than transit officials expected, and it happened much too quickly.

By no means is the entire mass transit system overburdened, but now many choke points -- both those that existed before the attack and others created by it -- are dangerously strained, creating conditions so intolerable that officials and business leaders fear they will drive businesses and people away from the New York area.

Undoubtedly the hardest hit is New Jersey Transit. Its trains make their way to New York's Pennsylvania Station through a single tunnel beneath the Hudson, one that the agency shares with Amtrak. With two train lines, the tunnel has long operated at capacity. After the terrorist attack, for a sum that New Jersey officials would not disclose, Amtrak ceded a small amount of rush-hour time to New Jersey Transit -- meaning four more inbound trains during the morning rush and four more outbound during the evening.

But even with those extra trains, the number of people standing every morning, pressed up against the windows or their neighbors, has grown to more than 23,000.

Those conditions mean that a longstanding plan to relieve serious crowding is now in serious jeopardy. The agency had planned to open the Secaucus Transfer Station next fall, allowing riders from Bergen County to transfer to trains going directly to Manhattan.

But the switch would mean an extra 16,000 passengers boarding Manhattan-bound trains, a scene no one now even wants to imagine, especially as New Jersey Transit considers a fare increase of about 10 percent to help close multimillion-dollar budget deficits.

The agency would love to encourage more of its riders to switch to buses. But New Jersey Transit commuter buses already carry about two-thirds of all the agency's passengers and, as with the trains, the system is full. No more gates are available at the Port Authority for the agency's buses, and Jeffrey A. Warsh, the executive director of New Jersey Transit, said no more buses could go through the Lincoln Tunnel at the height of the morning rush.

Before Sept. 11, 14,000 people were already standing on buses; now there are more than 16,000.

"It's amazing what people have to endure," Mr. Warsh said. "New riders are going to come out and say, `Oh, my God. I can't deal with that. I can't get a seat. I can't even get on the train.' "

Part of the problem is that thousands of jobs have moved to Midtown. The transit lines pouring people into the area have become like a funnel trying to direct too much water. New Jersey Transit officials have estimated that of the financial jobs that survived the attack and moved from Lower Manhattan, 60 percent relocated to Midtown.

The agency's projections show that even with the opening of a temporary PATH station at the World Trade Center site in about two years, the station would initially siphon away only about 2,000 of the 15,000 or so extra morning riders that New Jersey Transit has picked up.

If that projection is accurate, and more passengers will now be bound for Midtown or other parts of Manhattan, it also means trouble for the Port Authority, which runs the PATH. Although the line's ridership has dropped since the attack -- to 205,000 passengers a day, compared with 257,000 before -- it has not dropped as much as officials thought it would, with two of the system's 13 stations closed.

The tiny Christopher Street station once handled an average of 3,700 passengers a day; now it handles 8,000. The crowds at Ninth Street and 14th Street have slightly more than doubled, and -- suggesting the job shift to Midtown -- the number using the 33rd Street station has increased to 45,000 from 28,700.

That kind of extra crowding on the PATH has largely not occurred on the New York City subway system after the attacks, because ridership was already slowing and the subway was able to restore service to all but four stations in Lower Manhattan. But with train routes mostly back to normal again, the subway must now deal with a new problem in a much less secure city: safety.

In September, the number of subway delays caused by police investigations of suspicious packages or white powders jumped to 458, more than double the total from the month before the terrorist attack. By October, police delays more than quadrupled, to 2,648, making them by far the leading cause of late subway trains, as reports of suspicious packages and white powders flooded in.

Those disruptions have started to ease, transit officials say. There has not been another incident approaching the one on the morning of Oct. 22, when an investigation of a white powder at 34th Street and the Avenue of the Americas delayed 234 trains on five lines.

"Things seem to be heading back in the right direction," said Al O'Leary, the chief spokesman for New York City Transit.

But, in November, the leading cause of subway delays was still listed as "suspicious substances." Subway officials caution that riders must change their expectations about the balance between security and trains running on time.

Iris Weinshall, the city's transportation commissioner, said that on the roads around the city, drivers have changed their expectations, and their behavior, more quickly than planners thought. One change, revolutionary in itself, is simply that drivers now do not expect to be able to drive whenever they want.

Two reasons are the continuing security checkpoints and unexpected road closures that can still make driving a harrowing experience. But the ban on single-occupant vehicles crossing into Lower Manhattan or Midtown from 6 to 10 a.m. has had a profound effect, resulting in a 15 percent drop in traffic on those crossings in the morning.

That result, which has greatly reduced gridlock around the region, could mean that the ban will stay in place well into this year.

"The drumbeat is going to be there to lift the S.O.V. ban, but what's going to happen if we lift it?" asked Ms. Weinshall, who added that her agency had commissioned an ambitious study of the effects of the restrictions on the city's economy and roads.

Many transportation experts say that if the ban remains, what will undoubtedly happen is a continued funneling of people onto mass transit -- and mounting worries about how the system can handle it.

For now, one of the only pressure valves can be found on the open water, where ferry ridership has surged to 124,000 passengers a day from 97,000 before Sept. 11, with nine new routes added in the last three months and new landings on the way.

Transit officials -- confronted with the huge capital investments and lead time necessary to improve rail service -- are also seriously looking at proposals to create what is known as "bus rapid transit." A kind of subway on the highways, this would be accomplished by rigidly separated bus lanes within and even into the city, where buses could travel much faster and load more the way subways do, at above-ground stations with turnstiles.

"There's a lot more ferment than there has ever been on many of these issues," said Mr. Kaehny, of Transportation Alternatives. "People are being forced to think outside of the box."

Many transportation experts call that kind of thinking imperative.

"People are willing to put up with those conditions for a week or a month or if they knew how long it was going to be," said Jeff Zupan, a senior transportation fellow with the Regional Plan Association, a nonprofit group that advises governments on development.

"But if they don't know how long it's going to go, they're going to start saying, `Why do I have to take this? Why do I have to live here?' "