President Bush's directive that bans the torture of terror suspects applies to all prisoners, even important Al Qaeda captives being held by the CIA (search) at secret camps in overseas countries, U.S. and foreign officials say.

It's believed that such secret detention facilities have existed — or still exist — in Thailand, Afghanistan, Guantanamo Bay and, according to a Washington Post article, at former Soviet compounds in Eastern Europe.

National Security Adviser Stephen Hadley would not confirm or deny the article's report but said all terror suspects are held under the anti-torture directive.

"A Geneva Convention detainee cannot be held secretly; that's why the president has determined that Al Qaeda and other terrorists are not subject to the Geneva Convention," Sen. Lindsey Graham (search) told FOX News.

Suspicions interrogators use water boarding, where detainees are held under water to the point where they believe they will drown, or other forms of torture are drawing increasing attention to overseas detainments.

"What I'm against is no matter where you hold them under what authority, you still got to have American values when you do interrogations," he continued.

"That will be applied by the CIA because that's an American value we need to apply to win this war."

According to the Washington Post article, the existence and locations of the facilities — referred to as "black sites" in classified White House, CIA, Justice Department and congressional documents — are known to only a handful of officials in the United States and, usually, only to the president and a few top intelligence officers in each host country.

“These are difficult issues,” said State Department spokesman Sean McCormack (search). “We have ongoing discussions on a variety of different fronts with countries around the world about these issues, because the threat from terrorism and these individuals who are committed to the use of terror is a common threat to democracies and peace-loving nations around the world, including the United States."

The CIA and the White House, citing national security concerns and the value of the program, have dissuaded Congress from demanding that the agency answer questions in open testimony about the conditions under which captives are held. Virtually nothing is known about who is kept in the facilities, what interrogation methods are employed with them or how decisions are made about whether they should be detained or for how long.

“This administration is shaming our nation by seeking backdoor mechanisms to skirt our obligations to prevent torture,” said Rep. Ed Markey (search), D-Mass.

“We cannot play games and devise creative legalisms to dodge our obligation to the U.N. Convention Against Torture (search), but that is exactly what Vice President [Dick] Cheney and this administration are determined to do. We must shut down this black hole for prisoners in which torture is allowed to thrive,” he said.

Earlier this year, when Pakistan captured Al Qaeda's operations leader, Abu Faraj al-Libbi, Pakistani officials told FOX News he had been turned over to U.S. officials for questioning, a claim the CIA refused to corroborate.

Al-Libbi joined a growing number of Al Qaeda (search) members who have allegedly been held in such secret detention facilities run by the CIA.

Some believe this strategy is designed to enable more effective intelligence-gathering in the War on Terror (search), reasoning that overseas operations grant interrogators more latitude when questioning suspects.

Among the first to be held in a so-called "black site" was Abu Zubaydah (search), the operations chief for Usama bin Laden. Zubaydah was captured in March 2002 in Pakistan and reportedly relocated to a "black site" in Thailand.

Later in 2002, Pakistani intelligence also detained Ramzi bin al-Sheib (search). Al-Sheib was the pay master for the Sept. 11, 2001 terror attacks who facilitated the logistics and financing of U.S. Al Qaeda cells from Hamburg, Germany.

Both operatives were significant catches because the intelligence community believed that questioning them would uncover more operatives and plots in progress.

Neither the CIA nor the Department of Justice (search) will publicly comment on these sites; however, it is widely known within intelligence circles that a decision was made after Sept. 11, 2001 to hold Al Qaeda members outside the United States in an effort to disrupt future operations.

And while the Defense Department has produced volumes of public reports and testimony about its rules and detention practices after the abuse scandals at Iraq's Abu Ghraib (search) prison and at Guantanamo Bay, the CIA has not acknowledged the existence of its black sites. To do so could open the U.S. government to legal challenges, particularly in foreign courts, and increase the risk of political condemnation at home and abroad, officials familiar with the program told the Washington Post.

But the revelations of widespread prisoner abuse in Afghanistan and Iraq by the U.S. military — which operates under published rules and transparent oversight of Congress — have increased concern among lawmakers, foreign governments and human rights groups about the opaque CIA system. Those concerns escalated last month when Vice President Cheney and CIA Director Porter J. Goss (search) asked Congress to exempt CIA employees from legislation already endorsed by 90 senators that would bar cruel and degrading treatment of any prisoner in U.S. custody.

Although the CIA will not acknowledge details of its system, intelligence officials defend the agency's approach, arguing that the successful defense of the country requires that the agency be empowered to hold and interrogate suspected terrorists for as long as necessary and without restrictions imposed by the U.S. legal system or even by the military tribunals established for prisoners held at Guantanamo Bay.

Since then, the arrangement has been increasingly debated within the CIA, where considerable concern lingers about the legality, morality and practicality of holding even unrepentant terrorists in such isolation and secrecy, perhaps for the duration of their lives.

Mid-level and senior CIA officers began arguing two years ago that the system was unsustainable and diverted the agency from its unique espionage mission, the Post said.

FOX News’ Catherine Herridge, Teri Schultz, Jessica Lanier and The Associated Press contributed to this report.