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The daring U.S. military raid that killed Osama bin Laden may have closed a chapter in America's long fight against terrorism, but it has raised other issues like whether waterboarding helped illicit key information that led the U.S. to bin Laden.

As with many national security issues that Attorney General Eric Holder has faced, there's no end to the complications, even in a time of good news. Here's NPR's Carrie Johnson.

CARRIE JOHNSON: The Justice Department barely took time this week to reflect on the death of the country's most wanted terrorist. Attorney General Eric Holder reminded his staff they need to be on guard against new attacks by al-Qaida. And on Capitol Hill, he fielded questions about the role of torture in the intelligence breakthrough that located bin Laden.

Mr. ERIC HOLDER (Attorney General): There was a mosaic of sources that led to the identification of the people who led to...

Representative DAN LUNGREN (Republican, California): I understand that. But were any pieces of that mosaic as the result of enhanced interrogation techniques?

Mr. HOLDER: I do not know.

JOHNSON: That was California Republican lawmaker Dan Lungren pressing Holder about whether terrorism suspects had disclosed key clues about bin Laden's messengers after being waterboarding or deprived of sleep.

That question still matters and not just for history. A special prosecutor is investigating whether any U.S. contractors can be charged with a crime for going out of bounds in their interrogations of detainees.

In an extended interview with NPR, Holder said he's been getting regular updates from that prosecutor.

Mr. HOLDER: He's made substantial progress and I'm pretty confident that we will have a decision from him in the not-too-distant future.

JOHNSON: The word can't come soon enough for the intelligence community, which has been spooked by the idea of a criminal prosecutor poking around in the shadows of its work.

Ben Wizner of the American Civil Liberties Union says he's waiting for that decision, too.

Mr. BEN WIZNER (Staff Attorney, American Civil Liberties Union): We need something that can help us reach some national consensus on whether these methods were appropriate, on whether they were legal, on whether they helped the country or not.

JOHNSON: This is hardly the attorney general's first searing experience with national security. It's been a month since he announced the trial of 9/11 mastermind Khalid Sheikh Mohammed would take place in a military courtroom at Guantanamo Bay, not Holder's preferred location, the federal courts in New York.

You lost, but you put up a good fight along the way.

Mr. HOLDER: I'm almost reluctant to say I lost as much as I got overruled, I got blocked.

JOHNSON: In Holder's mind, Congress is to blame for blocking money the Justice Department could use to transfer detainees to the U.S. for a trial.

Republican Congressman Peter King of New York told the WOR Radio Network he sees it another way.

Representative PETER KING (Republican, New York): If he feels that strongly about it then it's his moral obligation to resign.

JOHNSON: Holder says he never considered resigning in protest over the location of those trials. He's told friends he wants to stay through Mr. Obama's first term in office.

Mr. HOLDER: I'm certainly not going to serve two terms. You know, Janet Reno did that and how she did that is amazing to me.

JOHNSON: Holder says he'll stay as long as he can make a contribution and there are still plenty of things to do. Such as the choice of a new FBI director when the current director's term expires this fall.

Holder says the White House needs to get a nominee to the Senate later this month or by early June. That 10-year appointment will be a legacy issue for the Obama administration.

There are other legacies, too: its handling of the Guantanamo prison and its defense of the intelligence community and lawsuits over rendition and wiretapping. Both of those alienated human rights groups. But Wizner of the ACLU isn't pointing the finger at Holder.

Mr. WIZNER: The department has not been independent in the way that the Justice Department ought to be, but too often has been carrying out the political, not the legal objectives of the White House.

JOHNSON: Holder says he's had his share of disagreements with the White House and some degree of tension is natural. At the same time, Holder says he's part of a larger national security team that the president leads.

As for his decision to try Khalid Sheikh Mohammed in New York, Holder says he's still proud of the choice he announced 18 months ago.

Mr. HOLDER: I'm comfortable with it not only for the way it looked in November of 2009, but how it'll look 50 years from now.

JOHNSON: Holder says he's speaking to history.

Carrie Johnson, NPR News, Washington.

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