Dozens of suspected terrorists may have been mistakenly allowed to enter the U.S. as war refugees, according to FBI agents who are investigating roadside bombings in Iraq and Afghanistan.

The 2009 discovery of two al Qaeda-trained terrorists living as refugees in Bowling Green, Kentucky, prompted the FBI to assign hundreds of specialists to check its archive of improvised explosive devices in war zones for other suspected terrorists’ fingerprints.

That pair eventually admitted to attacking U.S. soldiers in Iraq, and Rep. Michael McCaul (R-TX) said he wouldn’t be surprised if there were many more living in this country.

“These are trained terrorists in the art of bomb-making that are inside the United States, and quite frankly, from a homeland security perspective, that really concerns me,” said McCaul, chairman of the House Committee on Homeland Security.

The State Department stopped processing Iraqi refugees for six months in 2011, following the Kentucky case, even some who’d helped U.S. forces as interpreters or intelligence assets.

One of those Iraqis who’d assisted American troops was assassinated before his refugee application could be processed.

Fewer than 10,000 Iraqis resettled in the U.S. as refugees in 2011, half the number from the year before, according to the State Department.

Most of the more than 70,000 Iraqi refugees living in the U.S. are law-abiding immigrants eager to start a new life in America, state and federal officials said, but the flawed system that was overhauled two years ago allowed some insurgents into the country.

"How do you have somebody that we now know was a known actor in terrorism overseas, how does that person get into the United States? How do they get into our community?" wondered Bowling Green Police Chief Doug Hawkins, whose department assisted the FBI.

Department of Homeland Security spokesperson Peter Boogaard said the U.S. government continually tries to improve its procedures for vetting immigrants, and he said the process considers more information than ever.

"Our procedures continue to check applicants' names and fingerprints against records of individuals known to be security threats, including the terrorist watch list, or of law enforcement concern,” Boogaard said. “These checks are vital to advancing the U.S. government's twin goal of protecting the world's most vulnerable persons while ensuring U.S. national security and public safety," the statement said.

A Department of Homeland Security senior intelligence official testified last year in a House hearing that Waad Ramadan Alwan and Mohanad Shareef Hammadi's names and fingerprints were checked by the FBI, DHS and the Defense Department during the vetting process in 2009 and "came in clean,” permitting them to enter the U.S.

After the FBI received the intelligence tip later that year, a sting operation was set up in Kentucky to bait Alwan using an undercover operative recruited by the FBI, who offered him a chance to ship heavy arms to al Qaeda in Iraq.

The FBI wanted to know if Alwan was part of a local terror cell, and authorities became alarmed when he asked a relative who was also living in Bowling Green to help.

Federal agents secretly recorded Alwan brag to the informant that he’d built at least a dozen bombs in Iraq and killed American soldiers using a sniper rifle.

Alwan even sketched out IED designs that experts said clearly demonstrated his high level of skill.

Forensic experts found several of Alwan’s fingerprints on other devices stored in case files and alerted FBI agents in Louisville, who said that gave them proof the Iraqi had been involved in attacks against U.S. soldiers.

Prosecutors also said they recorded surveillance tape of Hammadi and Alwan discussing a plot to assassinate an Army captain they’d known in Iraq now that he was back in the U.S. and to possibly attack other American targets.

"Many things should take place and it should be huge," Hammadi told Alwan in an FBI-recorded conversation, which a prosecutor revealed at Hammadi's sentencing last year.

President Barack Obama was briefed on the case in early 2011 as agents decided whether to arrest the pair right away or continue arranging phony arms shipments to Iraq, including machine guns, explosives and secretly deactivated Stinger missiles.

But once FBI agents determined no other conspirators were involved, they arrested the pair just weeks after Osama bin Laden was killed in Pakistan.

The pair agreed to plead guilty to supporting terrorism and admitted to their al Qaeda connections.

Alwan was sentenced to 40 years in federal prison and Hammadi was sentenced to life, although he’s appealing the sentence.

"We need to take this as a case study and draw the right lessons from it, and not just high-five over this," said retired Army Lt. Gen. Michael Barbero, former head of the military's Joint IED Defeat Organization. "How did a person who we detained in Iraq -- linked to an IED attack, we had his fingerprints in our government system -- how did he walk into America in 2009?"

Barbero helped use the Kentucky case to get funding for an FBI fingerprint lab that focuses on examining fingerprints found on the 100,000 IED remnants kept in a huge warehouse in Washington to matching them against foreign nationals seeking refuge in the U.S. or suspected terrorists living elsewhere.

Watch this video report posted online by ABC News:

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[Image via Agence France-Presse]