President Obama said he would not interfere in the legal process
President Obama has rejected a request by seven former heads of the CIA to end the inquiry into allegations of abuse of suspects held by the agency.
"Nobody's above the law," Mr Obama said in an interview with the American CBS television programme Face The Nation.
The US Attorney General Eric Holder last month named a prosecutor to examine whether the CIA had gone beyond approved interrogation methods.
The former heads wrote to Mr Obama saying the probe would hamper CIA work.
They said the cases had already been investigated during the Bush administration and lawyers had declined to prosecute in all but one.
"This approach will seriously damage the willingness of intelligence officers to take risks to protect the country," their letter read.
"In our judgment, such risk-taking is vital to success in the long and difficult fight against terrorists who continue to threaten us."
The former CIA chiefs served under Republican and Democratic presidents.
Beyond Bush era
But Mr Obama made clear he would not intervene in the judicial process.
"I appreciate the former CIA directors wanting to look after an institution that they helped to build," he told CBS.
"But I continue to believe that nobody's above the law. And I want to make sure that, as president of the United States, I'm not asserting in some way that my decisions overrule the decisions of prosecutors who are there to uphold the law."
President Obama made clear that he has consistently said he wants to look beyond the Bush administration, which human rights groups have accused of using torture to gain information from suspects in violation of US and international law.
The inquiry into alleged prisoner abuse was announced in August
Bush-era officials, including former Vice-President Dick Cheney, have defended their actions and said interrogations yielded valuable intelligence.
Mr Obama said that the attorney general had to make a judgment about what happened.
"My understanding is it's not a criminal investigation at this point. They are simply investigating what took place," he said.
"I don't want witchhunts taking place. I've also said, though, that the attorney general has a job to uphold the law."
The attorney general's spokesman Mark Miller has said Mr Holder does not believe his investigation will affect CIA employees' commitment to their work.
"The attorney general's decision to order a preliminary review into this matter was made in line with his duty to examine the facts and to follow the law.
"As he has made clear, the department of justice will not prosecute anyone who acted in good faith and within the scope of the legal guidance given by the Office of Legal Counsel regarding the interrogation of detainees," Mr Miller said in a written statement.
The seven former CIA directors also warned that foreign governments could be hesitant to co-operate with the US if the inquiry continues.
The current CIA Director Leon Panetta was not a signatory to the letter, but he opposed Mr Holder's investigation.