Michael Hayden told the Senate Intelligence Committee at his confirmation hearing on Thursday that the programme had been designed to ensnare terrorists, not spy on ordinary people.
"Clearly the privacy of American citizens is a concern constantly. We always balance privacy and security," he said.
Hayden was asked as many questions about the National Security Agency - the super-secret agency he led from 1999 to 2005 - as about his visions for the CIA.
Senators grilled him on the NSA's eavesdropping without warrants on conversations and emails believed by the government to involve terrorism suspects, and reports of the tracking of millions of phone calls made and received by ordinary Americans.
Hayden said that after the attacks of September 11, 2001, George Bush, the US president, decided that more anti-terrorism surveillance was necessary than the NSA had been doing.
He said the surveillance programme used a "probable cause" standard that made it unlikely that information about average Americans would be scrutinised.
But he declined to openly discuss reports that the NSA was engaged in broader surveillance, including a story in USA Today that the NSA has been secretly collecting phone-call records of tens of millions of US citizens.
Under questioning from a Democratic senator, Carl Levin, Hayden said he would only talk about the part of the programme the president had confirmed, without confirming whether that was indeed the whole programme.
Hayden was asked about reported friction between him and Donald Rumsfeld, the defence secretary, over how the NSA and other intelligence agencies would work with the Pentagon.
Hayden acknowledged faults in
intelligence before the Iraq war
Some critics have suggested that Hayden, 61, who remains an active general, is too closely aligned with the Pentagon to objectively run the civilian CIA.
Hayden declined to answer questions by Dianne Feinstein, a California Democratic senator, saying he would answer them later in a closed-door session.
They included whether he believed that "waterboarding", in which prisoners are strapped to a plank and dunked in water until nearly drowning, was an acceptable form of interrogation. He also declined to say publicly how long he believed the United States could hold terror suspects without a trial.
Meanwhile, the White House spokesman, Tony Snow, expressed the president's full confidence in Hayden. "The guy's got a record of trying to take on big reform tasks and carrying them out," Snow told reporters.
Hayden acknowledged a series of intelligence failures in the run-up to the US decision to invade Iraq and promised to take steps to guard against a repeat of such errors.
"We just took too much for granted. We didn't challenge our basic assumptions," he told the Senate committee.
The committee chairman, Senator Pat Roberts, complained about the CIA's performance on Iraq. While "nobody bats 1,000 in the intelligence world," Roberts cited "a terribly flawed trade craft" in the CIA's intelligence.