By Brian Donohue,The Star-Ledger (Newark, N.J.)

As the Japanese cruise ship Topaz sat docked at a Manhattan pier in July, Endang Rusmindar walked off with a visa that allowed him to spend a day on shore.

When the crew shoved off two days later, Rusmindar, an Indonesian national and a waiter on the ship, was nowhere to be found.

He still may be in the United States.

He may have gone to Canada or flown to another country.

The federal government has no way to know.

Four years after the Sept. 11 attacks, the U.S. government still can’t track an estimated 3 million visitors currently in the country who have overstayed their visas. Such gaping holes, security experts say, expose the nation to a constant risk even as it spends billions to maintain its borders.

It wasn’t supposed to be this way.

Seven years after its initial deadline, the system mandated by Congress to track people like Rusmindar – called U.S. Visitor and Immigrant Status Indicator Technology, or US-VISIT – is only partially in place.

US-VISIT does collect fingerprints and digital photos of millions of visitors when they arrive at 115 airports and 15 seaports. And those checks have nabbed 820 wanted criminals or immigration violators, preventing them entering the country, Department of Homeland Security officials said.

What it fails to do is screen about 78 percent of visitors to the United States.

In fact, the complete system envisioned by Congress, one that also would collect data from people leaving the country and the hundreds of millions of people who come here from Mexico and Canada, remains years, and untold billions of dollars, away from completion.

“If you take it from Pearl Harbor to V-J Day, we were able to win World War II faster than we’ve been able to do some of these pilot projects,” said Rep. Dan Lungren, R-Calif., the chairman of the congressional committee overseeing US-VISIT.

Despite the missed deadlines, Homeland Security officials say the program has been a success, reminding critics that the nation has never undertaken such a massive effort to monitor its borders. For the first time, foreigners arriving at airports are having their identities confirmed and their backgrounds checked.

“US-VISIT has been extremely successful in fulfilling its mission,” wrote Jim Williams, program manager for US-VISIT, in response to a February report by federal auditors. “It represents the greatest advance in border technology in three decades.”

US-VISIT has two goals: to keep visitors from overstaying their visas and preventing terrorists and criminals from entering the country.

So far, the system appears to have improved the government’s ability to crack down on people who overstay. More than 10,000 people have been denied visas based on data collected from US-VISIT. Government analysts also say they are getting a better grip on which countries and which types of people are more likely to violate immigration laws.

But a growing chorus of critics say there still will be too many holes to stop terrorists once the system is completed.

“For those who don’t want to be tracked, there are a few too many ways of getting around it,” said Rey Koslowski, a former Rutgers University professor who studied the system before transferring to the State University of New York this fall. “It’s providing reassurance to the traveling public, perhaps, but whether or not it has added value, I don’t know.”

Once the system is completely up and running, US-VISIT will still enroll only a small percentage of visitors to the United States. That’s because the two largest groups of border crossers, Mexicans with special U.S.-issued border crossing cards and Canadian citizens, remain exempt.

Of the 440 million people who cross U.S. borders each year, 358 million cross by car, bus, truck or foot across the land borders with Mexico and Canada.

Border guards perform a quick visual inspection of a driver’s license, passport or border crossing card, which allows Mexican holders to travel within 30 miles of the border. If a driver or passenger is a non-U.S. resident from a country requiring a visa, they are further inspection.

For now, those pulled over for “secondary inspection” are fingerprinted and photographed at 50 land borders. By the end of the year, the system should be in place at all 165 crossings, Homeland Security officials predict.

Critics call the exclusion of Canadian and Mexican visitors the single largest gap in US-VISIT. Terrorists or lawbreakers can forge or steal a border crossing card or passport to enter uninspected.

“If I were going to look for a soft spot, if I were a terrorist, that would appear to be a soft spot,” said Lungren, the California congressman. “It is probably too inefficient to require that of (Canadians and Mexicans), but I would say we’d better take another look.”

But enrolling Canadians and Mexicans likely would anger both governments, as well as U.S. businesses that rely on a smooth flow of people and goods across the borders.

It also would require a huge investment to widen border crossings, hire new inspectors, build tollbooths, even widen bridges to keep traffic flowing.