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GUY RAZ, host: The scandal over a botched gun trafficking investigation has caused a shakeup at the Bureau of Alcohol, Tobacco and Firearms. And now, attention is shifting to the top ranks of the Justice Department. This week, the Republican chairman of the House Judiciary Committee called for an independent council to investigate. He wants to know if the attorney general misled Congress about the operation known as Fast and Furious. The program went horribly wrong when ATF agents lost track of hundreds of weapons, as they moved along the Southwest border.

NPR's Carrie Johnson has the story.

CARRIE JOHNSON: Old hands in Washington know it's never a good sign when the president of the United States has to make a statement like this one.

President BARACK OBAMA: I have complete confidence in Attorney General Holder, in how he handles his office.

JOHNSON: That's Mr. Obama responding to questions from reporters today about his faith in Attorney General Eric Holder. Holder is in the spotlight because of emails and other Justice Department documents the White House released to Republicans in Congress that show the Holder seems to have known about the gun-trafficking operation known as Fast and Furious much earlier than he said.

Here's the attorney general under questioning from California Republican lawmaker Darrell Issa in March of this year.

Representative DARRELL ISSA: When did you first know about the program officially, I believe, called Fast and Furious? To the best of your knowledge, what date?

ERIC HOLDER: I'm not sure the exact date, but I probably heard about Fast and Furious for the first time over the last few weeks.

JOHNSON: The new documents show Holder received five weekly updates on the operation starting in July 2010. But the Justice Department says Holder meant he learned about the ATF's failure to monitor the weapons only earlier this year. Issa, talking with MSNBC this week, says he isn't buying it.

ISSA: There may be an explanation that partially vindicates him. In other words, he may not have committed perjury but he certainly failed in his duty of candor, because he did know the name a year before that.

JOHNSON: Two people have already lost their jobs over the scandal: The head of the ATF and U.S. attorney in Arizona, where the Fast and Furious operation played out. And this week, the new chief of the ATF followed through on a promise and overhauled his management team.

But the shakeup won't make this scandal go away. The Justice Department's inspector general is investigating the Fast and Furious Operation, and who at the Justice Department knew about the questionable tactics that agents were using.

Holder told reporters last month that senior Justice Department officials didn't know ATF had lost track of guns.

HOLDER: The notion that somehow or other that this thing reaches into the upper levels of the Justice Department, is something that at this point I don't think is supported by the facts.

JOHNSON: The White House is continuing to turn over documents to Republicans in Congress, including emails that suggest the ATF used similar strategies during the last Bush administration. But Republicans leading the investigation say the Bush-did-it-too defense doesn't fix the problem of what this attorney general knew and when.

Carrie Johnson, NPR News, Washington.

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