People wait in a security line at John F. Kennedy Airport in New York City. (Spencer Platt/Getty Images)

The nation’s crowded transportation system is already feeling the effect of billions of dollars in automatic federal budget cuts, with long waits at some international airports and signs that cargo may begin stacking up on seaport docks because inspectors are working fewer hours.

Up to 40 percent of the customs booths at airports in New York and Miami were unmanned over the weekend because of cutbacks in overtime for customs officials, resulting in waits of up to three hours for international passengers, Customs and Border Protection officials said. In Long Beach, Calif., the nation’s second-busiest cargo port, customs officials are working 90 minutes less per shift, which could lead to longer processing times for containers.

The slowdowns are among the first tangible effects of the automatic budget cuts known as the sequester, which began to take effect Friday and will carve $86 billion from domestic and defense programs over the next seven months. On Tuesday, the Obama administration announced that the impact had reached the White House, which has canceled public tours starting Saturday because of the sequester.

Art Wong, a spokesman for the Port of Long Beach, which handles 40 percent of the nation’s imports, said uncertainty about how the cuts will affect operations makes it difficult to plan.

“We’re not sure where this is going to go,” he said. “There are a lot of people whose jobs depend on this [port].”

Wong said that factory shutdowns tied to New Year’s celebrations in China mean there is a lull in the volume of goods moving through the Long Beach port, which handled $155 billion in cargo in 2011. But operations are expected to pick up in the next few weeks, he said.

Officials at the National Retail Federation said they have been told that the cutbacks could mean delays of up to five days or more in moving containers through ports. That would mean longer waits for retailers expecting spring merchandise as delays ripple through the transportation system.

“We’re hoping the impact is going to be minimal, but it’s too tough to say at this time,” said Jonathan Gold, vice president for supply chain and customs policy at NRF.

But some airports already are feeling the pinch, and customs officials warned Tuesday that delays would worsen in coming weeks.

“Under sequestration, U.S. Customs and Border Protection will not be able to maintain its required staffing levels at our ports of entry,” the agency said in a statement Tuesday, adding: “In the coming weeks we will see additional impacts as the CBP hiring freeze and furloughs take place. . . . Itineraries should be adjusted to account for unexpected delays.”

In addition to Miami and New York, customs officials said there were delays for international passengers moving through Chicago’s O’Hare International Airport, although airport officials there said they could not confirm the problems.

Mark Henderson, a spokesman for Miami International Airport, said that on Saturday — the airport’s busiest day for international travel — passengers who would normally wait an hour to clear customs spent up to three hours in line. Customs officials said passengers aboard 51 flights that landed in Miami waited more than two hours, while those on four flights had wait times of more than three hours.

Henderson said it’s still too early to tell whether this past weekend was an anomaly or a sign of things to come. He said customs lines had returned to normal by Monday.
“It’s important that our first-timers get a good impression,” he said of wait times. “Airports are the front door of the community.”

At New York’s John F. Kennedy International Airport, customs officials said weekend passengers from approximately 56 flights had wait times of more than two hours and those on 14 flights waited more than three.

The delays were mostly limited to weekend travelers and have primarily affected international passengers moving through customs, officials said.

Locally, officials at Reagan National, Dulles International and Baltimore-Washington International Thurgood Marshall airports said the cuts have not had an immediate effect on passenger wait times.

Customs and border officials said delays will become widespread as the department begins furloughing employees. Officials at the Department of Homeland Security — which includes customs and border protection officers as well as Transportation Security Administration screeners — said furlough letters are expected to go out to employees on Thursday.

On Monday, Homeland Security Secretary Janet Napolitano said during a Politico event that wait times at some airports were “150 to 200 percent as long as we would normally expect.” She cited airports in Los Angeles, Atlanta and Chicago as examples, although she said she would have to check to be certain.

Democratic lawmakers and the White House have used the specter of long security lines and delayed flights to make their case that the mandatory budget cuts put into place because of the sequester are a bad idea. Many Republicans have pushed back, demanding more information and arguing that agencies such as the Federal Aviation Administration are able to absorb spending reductions without compromising the safety or efficiency.

Napolitano said the public should prepare for longer waits in coming days as the impact of the sequester begins to ripple throughout the system.

At TSA, where a hiring freeze is expected to be put into place, officials anticipate there will be 1,000 security officer vacancies by Memorial Day weekend. That number could grow to 2,600 by the end of the fiscal year. Cutbacks at the FAA also could mean flight delays if fewer air-traffic controllers are staffing airport towers, officials said.

As a result, transportation officials said, current wait times of 30 to 40 minutes could double at the nation’s largest airports during busy travel periods. Even those flying at non-peak times can expect longer waits, officials said.

Even if waits are not as lengthy as feared, travel industry representatives worry that chronic delays could still have a serious impact.

“We’re a perception-related business,” said Geoff Freeman, president of the U.S. Travel Association. “If it’s the perception, it becomes the reality and travelers may go and spend their money somewhere else.”

Tara Bahrampour contributed to this report.