A grand jury in Bowling Green charged Waad Ramadan Alwan, 30, and Mohanad Shareef Hammadi Alwan, 23, last month with 23 counts, including conspiracy to send weapons and money to Al Qaeda in Iraq. Alwan is also facing charges of attacking U.S. troops in Iraq. Both face life in prison if convicted. A trial has yet to be scheduled for them.
McConnell says the two belong in Guantanamo, regardless of whether they were detained on U.S. soil or foreign land, a distinction used by the Obama administration to establish venue.
"A few years ago, we set up military commissions for the specific purpose of trying foreign terrorists," McConnell told Fox News. "The perfect place for these terrorists is at Guantanamo, to be interrogated and, if subsequently a trial is deemed appropriate for these foreign terrorists, there are courtrooms down there for the military commission trials. There is really no reason to be mainstreaming these foreign terrorists into a regular U.S. court."
McConnell said prosecuting the two in Kentucky poses security problems for the city of Bowling Green, including the cost of protecting the judge and jury.
"There's no reason in the world to be subjecting any American city to all of the complexities and security problems related to trying a foreign terrorist in a U.S. court," he said.
But the Justice Department disagrees.
"We are prosecuting these two alleged terrorists in federal court because it is the most proven method for keeping our country safe," Justice spokesman Dean Boyd said in a statement to FoxNews.com.
"Every single suspected terrorist taken into custody on American soil -- before and after the September 11 attacks -- has first been taken into custody by law enforcement -- not the U.S. military," he said. "Our criminal justice system provides all the authority and flexibility we need to effectively combat terrorist threats from individuals living within our borders."
Boyd noted that since the Sept. 11 terrorist attacks, hundreds of suspects have been convicted of terrorism or terrorism violations in federal courts across the country.
"In not a single instance, has a judicial district handling one of these terrorism prosecutions been subject to retaliatory attacks by terrorists, and the suggestion that federal, state or local law enforcement are incapable of ensuring a safe trial is an insult to law enforcement," he said. "On the other hand, there has never been a military commission prosecution at Guantanamo Bay of a terror suspect arrested on American soil."
Alwan and Hammadi were arrested in May after the FBI had launched an undercover investigation into Alwan in September 2009. The agency says it later identified two of his fingerprints on an unexploded IED recovered by U.S. forces in Iraq.
McConnell praised the Feds for their work but said the Justice Department was making a mistake in treating the case as a U.S. law enforcement matter rather than a foreign terrorist issue.
"Yeah, they were captured in the United States. It was terrific work done by the Justice Department and the law enforcement agencies. And all of that evidence that's been gathered would be useful in the military commissions," he said.
The prison facility at Guantanamo Bay has been a political football since the Bush administration began sending captured suspects to the military base in 2001. President Obama has vowed to close the detention facilities there, where roughly170 detainees remain, but met stiff resistance from Congress, and effectively reversed its position by allowing Khalid Sheikh Mohammed, architect of the Sept. 11 attacks, and his four co-conspirators to be tried by military commissions.
A spokesman for McConnell wouldn't say specifically whether the senator is considering taking legislative action.
"We're reviewing all options," he told FoxNews.com.