The Department of Homeland Security has made only a small dent in dealing with the millions of immigrants who have illegally overstayed their visas, despite the fact that several Sept. 11 hijackers were able to remain in the country by doing just that.

The finding was one of many outlined in a new report this week by the Government Accountability Office measuring progress at the department created in the wake of the 2001 terror attacks.

The report lauded DHS for making strides in building up the comprehensive and massive security department but said a number of "gaps and weaknesses" remain that must be addressed. GAO reported that about half of its 1,500 recommendations have been implemented, while others are still in progress.

"Eight years after its establishment and 10 years after the September 11, 2001, terrorist attacks, DHS has indeed made significant strides in protecting the nation, but has yet to reach its full potential," the report reads.

The finding on overstays highlighted a key problem which DHS has endeavored to address, to limited success.

Jack Martin, special projects director at the Federation for American Immigration Reform, said DHS won't be able to effectively root out overstays until it has a comprehensive system for monitoring who is exiting the country -- something GAO said the department lacks.

"They really don't have a starting point," he said.

According to the Sept. 11 commission, created after the attacks to determine security and communication weaknesses within the U.S. government, at least six of the Sept. 11 hijackers violated immigration laws while in the United States. Of them, at least four had overstayed their visas along with committing other violations.

Hijacker Nawaf al Hazmi overstayed his visa by nine months. Satam Suqami overstayed by four months. Neither overstay was detected by immigration authorities. Separately, ringleader Mohamed Atta and Marwan al Shehhi overstayed their visas after arriving in 2000 to attend flight school. Officials flagged the two after they left the U.S. and tried to return in early 2001, but apparently only because they were returning to finish flight school carrying tourist -- as opposed to student -- visas. They were admitted.

Following a prior GAO report, a Homeland Security official in July said the department would be going through a list of nearly 760,000 potential visa overstays to determine whether those individuals are in fact still in the country and if they pose a security risk. At the same time, administration officials recently made clear that they plan on exempting from deportation certain illegal immigrants who don't pose a threat and haven't committed a crime.

GAO Comptroller Eugene Dodaro, testifying on Capitol Hill Wednesday, said the problem of overstays still remains.

"I know that this is a very difficult task, but the overstays issue is significant," he said. "This is something that's a big challenge, but needs to be addressed going forward."

He said between 4 million and 5 million people in the U.S. have overstayed their visas. According to the GAO report, DHS field offices made just 8,100 arrests as a result of overstay investigations between 2004 and 2010. Further, the report said the department devotes about 3 percent of its investigative hours to overstay issues.

Muzaffar Chishti, a senior fellow at the Migration Policy Institute, highlighted the improvement that the government has made in cracking down on illegal immigrants since the Sept. 11 terrorist attacks.

"We're making huge advances in apprehension, detention and removal of people compared to 10 years ago," he said, noting that 380,000 illegal immigrants were deported last year compared to 1,000 in 1984.

Chishti added that targeting overstays isn't as important from a national security point of view as keeping out dangerous immigrants before they arrive.

"Every enforcement machine has certain limited resources," he said. "The question is how are you going to spend the limited resources. Are you going to go after high-risk criminals or yes, someone who has overstayed but is a garden variety unauthorized alien. ... We clearly don't have the resources to do the both."

Martin said the hijackers at least would have stood a better shot of being caught today, namely because of the expansion of the Secure Communities program under which local jails can check the immigration status of those they arrest. But Martin noted that's a "passive" way of catching illegal immigrants who might be dangerous.

But Roberto Lovato, a writer and member of Presente.org, which strongly opposes Secure Communities and organizes protests of U.S. immigration policy, said current enforcement measures don't make sense especially since the perpetrators of the Sept. 11 attacks were mostly middle and upper-middle class, highly educated people.

Lovato said the result of those attacks has been a "draconian, racist and militarized" method of immigration enforcement.

"Your best bet is to have community policing. ... The community takes ownership of the means of safety. You produce safety by working together," he said, adding that individuals can detect among their own groups members who are behaving oddly.

"If you really had immigrant communities not being in fear of police and fear of law enforcement everywhere" then monitoring suspicious immigrants would be easier, Lovato said.

The GAO report called for the DHS to establish a "comprehensive" system for monitoring who is exiting the country, and improve screening so it meets all requirements for detecting explosives.

GAO praised DHS for expanding its screening programs to check passengers against terror watch lists, improving the E-Verify program to help employers check their workers' immigration status and make other changes. But the report noted that the sheer size of DHS -- which merged 22 agencies into one sprawling department -- has over the years contributed to "schedule delays, cost increases and performance problems."

A separate report on immigration policy since the Sept. 11 attacks also cited a series of alleged gaps that could harm security.

Like GAO's analysis, the report from FAIR noted the country lacks a comprehensive system for monitoring who is leaving the country.

"This means that DHS and the FBI are deprived of information on who continues to stay on in the United States when no longer authorized to do so. They do not know how many such persons there may be," the report said.

The report also criticized the administration for "selective immigration law enforcement." Under a policy outlined by immigration officials this year, the Obama administration is prioritizing the deportation of illegal immigrant criminals and others who pose a threat while urging agents to exempt certain classes of illegal immigrants.

However, Deputy Homeland Security Secretary Jane Holl Lute highlighted that policy Wednesday as a step forward.

"Our immigration laws, while in need of reform, are being enforced according to common sense priorities that we have set, which are to identify and remove criminals and those who are a threat to the American people," she said.