The LIFG carried out operations against the Libyan government, including at least four suspected assassination attempts against Gadhafi in the 1990s, and was also believed to be connected to a series of suicide bombings in Casablanca, Morocco, in 2003, the U.S. State Department reported. As relations between the U.S. and Gadhafi improved in the mid-2000s after Gadhafi agreed to dismantle the country's nuclear program and renounce terrorism, some LIFG leaders allegedly cultivated relationships with top al Qaeda leaders, including Osama bin Laden, and were suspected of funneling fighters to Iraq to carry out operations against U.S. soldiers.
The designation of the LIFG as a terror organization in 2004 was meant as a "gesture of solidarity" with the Libyan government to fight terrorism, according to a March 2011 congressional report. Last August, Libyan ambassador to the U.S. Ali Aujali told ABC News the LIFG was never connected to al Qaeda and did not carry out terrorist operations.
"They were only opposed to Gadhafi during his rule and paid the price for that by being oppressed by the regime," he said then.
The Human Rights Watch report claims the case of waterboarding took place around April 2004, months before the LIFG was declared a terrorist organization, but months after then-CIA director George Tenet told a congressional committee the extremist group had links to al Qaeda and was considered "an immediate threat" to the U.S.
'They Wouldn't Stop Until They Got Some Kind of Answer...'
The man who leveled the waterboarding accusation, Mohammed al-Shoroeiya, said he was subjected to it multiple times.
"While he was strapped to the board with his head lower than his feet, they would pour buckets of extremely cold water over his nose and mouth to the point that he felt he was going to suffocate," the report says. "When asked how many times this was done to him, [al-Shoroeiya] said 'a lot …a lot … it happened many times... They wouldn't stop until they got some kind of answer out of me.'"
Khalid al-Sharif, who was detained along with Al-Shoroeiya at the time in Afghanistan and described a similar experience but without the board, told Human Rights Watch it was "clear" they were in American custody and when he arrived at the facility, he was approached by a tall man "in uniform" who said he was American. The man said that they could kill al-Sharif there "no one will know," the report says.
A spokesperson for the Department of Defense told ABC News the description of the uniform provided by al-Sharif, which included a red beret, is "not consistent with any American military uniforms that I'm aware of." The spokesperson declined to comment further.
The controversial use of waterboarding and other so-called "harsh interrogation techniques" had been authorized under George W. Bush's administration but the methods were rejected by executive order by President Obama shortly after taking office in January 2009.
ABC News' Luis Martinez and Jason Ryan contributed to this report.