Brennan has been the administration's chief architect of so-called targeted killings and deadly drone strikes against al-Qaida militants, including U.S.-born Anwar al-Awlaki in Yemen.
Brennan said Awlaki had been linked to a number of attempts to commit terror against U.S. citizens.
"We only take such actions to save lives when there is no other alternative to mitigate that threat," Brennan said, adding officials agonize over trying to limit dangers to civilians.
In response to questioning, Brennan said when it was possible to capture a terrorist, the administration has never opted to use lethal force instead.
Asked whether he would consider a special U.S. court to oversee the evidence before drone strikes are launched against U.S. citizens acting as terrorists abroad, Brennan said, "It's certainly worthy of discussion," though protecting Americans has been "an inherently executive branch function."
Brennan said the United States remains "at war with al-Qaida and its associated forces."
Senators on both sides of the aisle pressed Brennan to provide more information to Congress if he is confirmed by the Senate.
Sen. Ron Wyden, D-Ore., a main critic of the program, said the drone operation shows "unfettered [presidential] power without checks and balances that is so troubling." Wyden said the U.S. Justice Department had not been following through with delivering the documents on the program that the committee had requested, and Obama had committed to providing.
Wyden asked Brennan to see what he could do to provide the documents.
He asked Brennan whether the administration should "give an individual American an opportunity to surrender" before being targeted as a terrorist.
"Any American that joins al-Qaida will know he has joined an organization that is at war with the United states," Brennan. He added that any member of al-Qaida "anywhere in the world" has an opportunity to surrender.
Brennan told the Senate Select Intelligence Committee, which is considering his nomination, the United States is under "daily cyberattack by nation states" and individual hackers.
He called the threat of cyberattack "one of the most insidious, one of the most consequential to our national security." Brennan said the role of the CIA was to determine the plans and intentions of foreign governments and groups that launch such attacks.
The CIA also must monitor nations trying to achieve nuclear weapons, he said.
Questioned about waterboarding, used against several terrorist detainees, Brennan said he was unaware of any information gained from the waterboarding technique that provided a "lead" in tracking down Osama bin Laden. Bush administration officials have cited waterboarding as a key element in tracking down bin Laden.
Bin Laden was killed by a SEAL team in his Pakistan compound in May 2011, in a operation carried out under the authority of then-CIA Director Leon Panetta.
Brennan promised to keep an open relationship with the committee. Sen. Barbara Mikulski, D-Md., said other than Panetta, "I feel I've been jerked around by every CIA director."
Before Mikulski's comment, Brennan said there had been a "trust deficit" between the CIA and the committee, but pledged to "make it my goal ... to strengthen the trust between us. ... You will get straight answers."
Under questioning from the panel's vice chairman, Sen. Saxby Chambliss, R-Ga., Brennan said he was not involved in the agency's "enhanced interrogation techniques" used on terrorist suspects, such as waterboarding, and conceded he at one time said such techniques "saved American lives."
Brennan said after reading part of a massive report from the committee that dealt in part with those techniques and criticized their usefulness, "I have serious questions about what [information] I was given at the time. ... At this point I don't know what the truth is."
Brennan told Chambliss he has no "second thoughts" about recommending against an attempt to capture Osama bin Laden in 1998. Brennan said he and all other CIA officials were against the attempt.
"I argued against that operation as well because ... its chance of success was minimal," he said.
Sen. Richard Burr, R-N.C., said the committee had requested documents relating to the Sept. 11 attack on the U.S. Consulate in Benghazi, Libya, that killed the U.S. ambassador and three other Americans.
"It is absolutely essential that we get the documents on Benghazi before you are confirmed," Burr warned.
Protesters disrupted the Senate panel's hearing several times as Brennan began his opening statement, prompting the panel chairwoman Sen. Dianne Feinstein, D-Calif., to order police to clear the hearing room. Spectators were then re-admitted one by one.
Feinstein, who said the panel still wanted eight opinions from the Justice Department's Office of Legal Counsel on the drone program, told Brennan the committee would hold a classified hearing with him behind closed doors Tuesday.
Earlier, Obama bowed to congressional demands for secret legal memos on targeted killings of U.S. terrorism suspects overseas, an administration official said.