While the Dubai Ports World deal focused public attention on security issues, those who make their living on the waterfront, and who rely on ships for transport, say the real problem is New York’s declining waterfront and the soaring transportation costs and tolls that businesses and consumers pay as a result.

The Port Authority ‘of New York and New Jersey, which has already moved most of the city’s maritime industry to the Garden State, is now threatening to shut down the last container port in Brooklyn, which is operated by American Stevedoring, Incorporated. A spokesman for the Port Authority, Steve Coleman, said the company will no longer be able to operate out of the Red Hook piers when its lease expires in a year.

Manhattan flourished because of its proximity to the ocean and deep water shipping channels; by the 20th century, New York was the busiest port in the world. Although traffic at the New Jersey ports is growing, overall the area is in decline- According to the American Association of Port Authorities, the combined Port of New York/New Jersey ranks 18th in the world in cargo volume. New York is the only major city in America where most of the freight arrives by truck.

Critics of the relocation of New York’s shipping business to New Jersey say it makes the ports less efficient, less accessible to the open sea, and less secure.

The owner of Hicool, a commercial food refrigeration company in Brooklyn, Yossi Banayan, said: “Every distributor I know in the kosher food industry goes to Newark to pick up containers of frozen food. When I go over there, most of the trucks have New York addresses on the door. In terms of the tolls, the driver salary, the fees, and gas, you are talking about hundreds of dollars for each trip. It’s a tremendous advantage when a shipment comes to Brooklyn.”

Several businessmen in Brooklyn expressed frustration that the products• they import, such as salmon from Chile, yogurt from France, and meat products from Israel, must be unloaded in New Jersey. Some businesses are forced to rent warehouse space in New Jersey so that USDA inspectors can check the foodstuffs there before they are trucked to New York.

“Our produce comes into various New Jersey ports, and we have to then truck it from Jersey to our facility here, or to cold storage,” the president of Acme Smoked Fish, Eric Caslow, said. “All of my facilities are in Brooklyn, so it would be much easier if the produce landed in Brooklyn because I would save in trucking costs.”

Mr. Caslow estimated that the trucking costs to Brooklyn from New Jersey add up to about a third of his total transportation costs.

“Rather than taking advantage of the easy access to shipping lanes, New York City planners have turned the islands of Manhattan and Long Island into a landlocked city where everything arrives by truck,” a spokesman for American Stevedoring, Matt Yates, said.

Even the railroads are dwindling on the east side of the Hudson River, and though roughly 40% of the cargo in America is moved by rail, in New York City the figure is only 2%. More trucks mean more damage to New York roads, added traffic congestion, and worsening air quality.

The Port Authority originally was created in 1929 to dig a rail freight tunnel under New York harbor to connect the Brooklyn ports with the train tracks in New Jersey that fanned out across the country. Instead, it ignored that mandate and moved the ports to Newark and Elizabeth, N.J. Cargo ships have to navigate the dangerous currents of the Kill van Kull, the narrow channel that separates Bayonne, N.J., from Staten Island, which is too shallow for larger ships to pass through safely.

“The Port Authority has failed to live up to its own mission,” the chairman of the New York State Conservative Party, Michael Long, said. “We need commerce shipments coming into New York City, and you couldn’t find a better location for that than the deep water ports in Brooklyn. The city should do everything it can to expand the port in Brooklyn for the future of commerce, jobs, delivery of goods and services.”

Rep. Jerrold Nadler and Mayor Giuliani tried to get the Port Authority to make good on its promise and build the tunnel, but instead the agency has spent $1.6 billion on dredging projects that include blasting through bedrock to deepen the Kill van Kull to 45 feet. However, the new generation of cargo ships plying international waters, called “postPanamax” vessels because they are too big to squeeze through the Panama Canal, need depths of more than 55 feet.

The deepening program also is facing environmental problems. Much of the mud that must be removed is contaminated with dioxin and other toxins from the Diamond Alkali Chemical Plant, which made Agent Orange during the Vietnam War. The toxins from the plant traveled downstream from the Passaic River into Newark Bay and the Kill van Kull.

Earlier this month, a U.S. Southern District judge, Shira Scheindlin, ruled that the dredging project violates federal law, and gave the Army Corps of Engineers four months to come up with a plan to clean up the mess.

An attorney for the National Resources Defense Council, Larry Levine, who filed the lawsuit, called the dredged mud from the Jersey waterways “a toxic soup.”

Even with a deeper channel, the Port Authority is planning to raise the clearance of the Bayonne Bridge between Staten Island and Bayonne so larger ships stacked with cargo could fit under it. Mr. Coleman said the authority has a drafted plan for a $500 million project to raise the bridge’s roadbed to 187 feet from 151 feet.

“It’s tough to imagine these larger ships going through those narrow, twisting channels, which already produces accidents, on their way to the New Jersey marshes,” the president of the National Maritime Historical Society, Peter Stanford, said.

Because the ships now navigating the Kill van Kull are the size of skyscrapers, if one of them sank in an accident or was the target of a terror attack, it could take months before the waterway was cleared. The Port of New York-New Jersey would be inoperable during that time.

Nevertheless, the Port Authority and the New York City Economic Development Corporation said it makes sense to keep the area’s maritime industry based in the ports of Newark and Elizabeth, N.J., because there is more dock and warehouse space. The authority also pointed out that it maintains a working port in New York at Howland Hook on Staten Island.

A spokeswoman for the EDC, Janel Patterson, said New York is still deciding what to do with the Red Hook terminal after it takes over the piers next year. The city is not overly concerned that most of the ports are located in New Jersey, she said.

“The rising tide lifts all ships. When opportunities increase in New Jersey, it helps places like Howland Hook and Brooklyn,” Ms. Patterson said.

But with Piers 1 through 6 set aside for Brooklyn Bridge Park, a new cruise ship terminal in Red Hook, and housing construction in Brooklyn, less space will be available for a container port.

Two years ago, the city of Baltimore faced a similar situation when what officials there called “condo creep” was taking up valuable space on the harbor. Baltimore passed a law that prohibited housing, hotels, offices, and restaurants along part of its waterfront, and created a Maritime Industrial District to be used specifically for shipping. At the time, the Baltimore planning director, Otis Rolley Ill, told the Associated Press, “Deep water access is a rare commodity, a finite commodity, and we’re doing everything in our power to protect it.”

“Baltimore was barricading itself in with apartments, cutting off access to the sea from its natural access to shipping channels,” Mr. Yates of American Stevedoring said. “It caught on that this was a mistake.”