Mr Obama said he had had no choice but to release the Bush administration's legal justification for interrogation techniques, which he considers to be torture - and has banned.
"Don't be discouraged that we have to acknowledge that potentially we've made some mistakes.
"That's how we learn. But the fact that we are willing to acknowledge them and then move forward, that is precisely why I am proud to be president of the United States and that's why you should be proud to be members of the CIA."
He also spoke of the public's appreciation of the work and "sacrifices" CIA staff make, emphasising that success was usually secret but failure often resulted in public blame.
He sympathised with those who work against unscrupulous enemies, but stressed it was important for national security that the agency did not overstep certain moral boundaries.
Quoting one of the memos, The New York Times said Khalid Sheikh Mohammed, the self-confessed planner of the 9/11 attacks, was subjected to the waterboarding technique, 183 times.
The method was used on another suspect, Abu Zubaydah, at least 83 times.
CIA 'still exposed'
BBC defence and security correspondent Rob Watson says this contrasts starkly with previous accounts given by US intelligence sources that implied both men told all after only the briefest exposure to the technique.
CIA staff applauded and cheered at Mr Obama's appearance
The new information could hardly have emerged at a more sensitive time for President Obama, our correspondent says.
Though highly critical during his election campaign of the CIA's methods, he adds, since coming to office Mr Obama has been anxious to boost morale at the agency and to draw a line under the controversies of its recent past.
The former head of the CIA, Michael Hayden, has said the release of the memos threatens national security by allowing prospective terrorists an insight into the precise limits of US interrogations.
He told Fox News network on Sunday that the release of the memos would make it more difficult to get useful information from suspected terrorists.
Other methods mentioned in the memos include week-long sleep deprivation, forced nudity and the use of painful positions.
Mr Obama on Thursday said he would not prosecute under anti-torture laws CIA personnel who relied in good faith on Bush administration legal opinions issued after the 11 September attacks.
But he has been criticised by human rights organisations and UN officials, who say charges are necessary to prevent future abuses and to hold people accountable.
This page is best viewed in an up-to-date web browser with style sheets (CSS) enabled. While you will be able to view the content of this page in your current browser, you will not be able to get the full visual experience. Please consider upgrading your browser software or enabling style sheets (CSS) if you are able to do so.