BOSTON – By the end of 2004, a monitoring system will allow the U.S. Coast Guard to track commercial ships to aid commerce and help secure the country’s coasts – including vulnerable seaports such as Boston – against terrorism.

The new system is part of the post-Sept. 11 push to secure the nation’s once-porous ports, increase efficiency of law enforcement, and boost oversight of maritime traffic in and out of the country’s 361 commercial shipping destinations, Vice Adm. James D. Hull said in an interview Friday with The Associated Press.

“This is to be sure that we have a visibility and transparency of who’s coming in, who they are, and we can hopefully push the borders out to take care of things away from shore,” Hull said.

Some larger ports such as Los Angeles, New York and Seattle have vessel traffic systems that, like the Federal Aviation Administration’s air traffic control system, allow the Coast Guard to track and manage maritime traffic.

The nationwide Automated Identification System, established by the Maritime Transportation Security Act signed into law last year, will be largely be used for monitoring, rather than managing, shipping.

Under the system, AIS transponders on commercial vessels will automatically send out information such as the size, direction and speed of the ships, making the data available to the Coast Guard and other ships. The system must be in place by the end of 2004.

Hull said American coastlines are far more secure than before Sept. 11. No ship enters U.S. waters today without the knowledge of maritime authorities and, when crises arise, officials can evaluate quickly and alert the highest echelons of government, Hull said.

“Now we know what’s coming into the country,” he said. “No ship comes in that’s of interest to us that we don’t check out at sea. You don’t want to find a problem in the middle of Boston.”

Still, gaps remain, and maintaining security and regulation of ports will require money, updates to the Coast Guard fleet, and new technology, Hull said.

“As we learned, after 9-11 we put everything we had on the waterfront of America, but we found that we didn’t necessarily have to have all that in some places,” he said. “Are there some gaps? Yes. Are we dealing with it and addressing it? Yes. But it’s not a one-year fix, it’s a multiyear fix.”

Hull also said that by 2005, Boston and other parts of New England will have in place a system that is being implemented around the country known as “Rescue 21.” The system will allow the Coast Guard to pinpoint distress calls, cut down on rescue time and thwart costly hoax calls.

The Coast Guard awarded a $611 million contract last year to General Dynamics of Scottsdale, Ariz., for the national distress system, which is already being used off the coast of Atlantic City and Virginia and is scheduled for completion in New York next year, and Massachusetts shores the year after that.

“The more I don’t do search and rescue, the more I have the same assets to do homeland security, and fisheries, and everything else,” he said. “The goal is to be smarter with what we have.”

The question of liquid natural gas storage, which came to the fore right after Sept. 11 when Mayor Tom Menino tried to block a huge LNG tanker from entering Boston Harbor because of security worries, also remains an issue of concern for Hull.

He said that the Coast Guard is reviewing numerous applications for new LNG facilities around the country, including one proposed for Fall River that would require tankers to travel up the Taunton River. Hull declined to say whether he supports or opposes that proposal, but said if he had his way, no LNG storage would be in cities.

“My personal preference is to build them offshore, because then it’s away from anybody, and it’s a little more protected,” he said.