"With respect to those who formulated those legal decisions, I would say that that is going to be more of a decision for the attorney general within the parameters of various laws and I don't want to pre-judge that," he said at a news conference with King Abdullah of Jordan in Washington on Tuesday.
"I do worry about this getting so politicised that we cannot function effectively and it hampers our ability to carry out critical national security operations."
Holder said in his confirmation hearings for the position of attorney-general last year that he considered waterboarding to be torture.
The documents released last week include justice department memos from 2002 and 2005 approving the CIA's use of "waterboarding", which simulates the sensation of drowning, sleep deprivation and other methods, all practices heavily criticised by human rights groups.
Obama also said that he would support a congressional investigation over the issue if it were conducted in a bipartisan manner.
"That would probably be a more sensible approach to take," he said.
"I think it's very important for the American people to feel as if this is not being dealt with to provide one side or another political advantage but rather as being done in order to learn some lessons so that we move forward in an effective way."
Obama has banned the use of waterboarding and other methods used under the Bush administration, saying that the US must stick to the army's field manual guidelines on the treatment of detainees.
Obama's comments come a day after Dick Cheney, the former US vice-president under Bush, criticised the decision by the Obama adminstration to release the documents.
Cheney told Fox News that the US had obtained valuable information from using such methods on so-called terror suspects following the September 11 attacks in 2001.
|Cheney: US obtained valuable information
from 'interrogation process' [EPA]
"One of the things that I find a little bit disturbing about this recent disclosure is they put out the legal memos, the memos that the CIA got from the Office of Legal Counsel, but they didn't put out the memos that showed the success of the effort," Cheney told the channel on Monday.
"I know specifically of reports that I read, that I saw, that lay out what we learned through the interrogation process and what the consequences were for the country."
Cheney also said he had made a formal request to the CIA to declassify memos to show the American people "what we obtained and what we learned and how good the intelligence was".
The dispute over the release of the memos, and over the Bush administration's use of waterboarding, intensified after it emerged the documents showed that CIA interrogators waterboarded Khalid Sheikh Mohammed, suspected of masterminding the September 11 attacks, 183 times.
One 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.