Obama said he understood CIA concerns that they were being asked to work under tighter regulations but that was what made the US "special".
"I understand that it's hard when you are asked to protect the American people against people who have no scruples, and would willingly and gladly kill innocents,'' the president said.
"I believe our nation is stronger and more secure when we deploy the full measure of both our power and the power of our values, including the rule of law. I know I can count on you to do exactly that,'' he said.
But the visit has been overshadowed by a New York Times report that CIA interrogators waterboarded Khalid Sheikh Mohammed, who has confessed to planning the September 11 attacks in New York in 2001, 183 times, according to an official document.
The 2005 US justice department memorandum also showed that Abu Zubaydah, an alleged al-Qaeda operative, was waterboarded 83 times, far more than the agency originally said, the Times reported on Sunday.
A former CIA officer had previously said Zubaydah had only been subjected to 35 seconds of waterboarding, which simulates the sensation of drowning.
Some critics have accused Obama of undermining the US intelligence community after he ordered the release of "top secret" memos on interrogation techniques that have largely been condemned as torture.
The memos document in detail techniques lawyers believed would not break laws against torture including waterboarding, the repeated slamming of a prisoner's head against a padded wall, face-slapping and sleep deprivation.
|Human rights groups have condemned the use
of waterboarding [AP - re-enactment]
Obama has banned the use of waterboarding and other harsh interrogation techniques used under the administration of George Bush, the former US president.
Michael Hayden, who was replaced as CIA chief earlier this year by Obama, has defended the agency's methods, saying: "We stand by our story. The critical information we got from Abu Zubaydah came after we began the EIT's [enhanced interrogation techniques]."
He said Zubaydah had "clammed up" after providing some "nominal information" under initial questioning, but under harsher interrogation he "gave up more valuable information" including tips that led to the capture of Ramzi Binalshibh, another senior alleged al-Qaeda agent.
Hayden also said the release of top secret memos were "really dangerous" for US intelligence efforts.
"Most of the people who oppose these techniques want to be able to say: 'I don't want my nation doing this', which is a pure honourable position, and 'they didn't work anyway'," he told the Fox News Sunday programme.
"The facts of the case are that the use of these techniques against these terrorists made us safer, it really did," he said.