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And now a story about two numbers and what they say about how the government is handling Islamic extremism in the U.S. One number keeps going down every year. The other number keeps going up. NPR's Ari Shapiro reports.

ARI SHAPIRO: The number that's more than doubled since 9/11 is FISA warrants, permission to spy on communications in the U.S. but while those spying warrants are more common than ever, prosecutions for Islamic extremists are becoming less common.

According to a study by the group Human Rights First, the Justice Department brought more than 20 indictments against Islamic extremists each year right after 9/11, and for the last couple of years, there have been just 10 of those cases annually.

So if spying is going up, and these prosecutions are going down, what exactly does that mean?

MONTAGNE: What it signals is that there has been a quiet revolution at the FBI in favor of conducting more prolonged intelligence investigations at the expense of preparing cases for potential criminal prosecution down the road.

SHAPIRO: That's David Laufman. He used to prosecute terrorism cases , and now he's in private practice. Tell me more about what you saw when you were leaving the U.S. Attorney's Office in the Eastern District of Virginia. This is the U.S. attorney's office that has prosecuted more terrorism cases than almost anywhere else. As you were leaving that department, what did you see coming down the pipeline?

MONTAGNE: I didn't see anything coming down the pipeline. It was clear by the time I left, in August, 2007, that there was a substantial decline in referrals of terrorism cases by the FBI to the U.S. attorney's office.

SHAPIRO: Laufman doesn't think that's just because there are fewer bad guys out there. He and others who have worked in the FBI and the Justice Department say the drop in these prosecutions reflects a fundamental shift in the government's approach to terrorism.

Michael Woods was chief of national security law at the FBI until 2002.

MONTAGNE: We're shifting toward a pre-emptive, preventative approach. So our emphasis on preventing future attacks, and I think what we're seeing is FISA being used to collect intelligence on potential threats.

SHAPIRO: Why isn't that intelligence being used to take someone down, charge them with a crime and lock them up so they don't do something?

MONTAGNE: You know, prosecution is kind of the last tool. It's - you know, you take the person out of circulation, but you also start rolling a public process that after a point you can no longer really control, and it becomes very public as to what you knew about this person, and that avenue of gathering more information or creating new sources is cut off.

SHAPIRO: And the government has other ways of taking people down that are less public than prosecutions. People can be deported or recruited as a source. Sometimes if an FBI agent just knocks on the door and says hello, that's enough to derail a terrorist plot, but the basic tension remains when to act and when to wait.

Pat Rowan is acting head of the Justice Department's National Security Division.

MONTAGNE: We're always looking at all these options, and we're weighing them. I don't think that I've been exposed to an instance where the FBI has said okay, well perhaps if we did a lot of work down this road, we'd be able to build a criminal case, but we're not going to pursue that because we're too busy collecting intelligence. That's not consistent with what I've seen.

SHAPIRO: But the FBI says sometimes it will resist a prosecution if the person they're watching keeps providing more-and-more valuable information.

MONTAGNE: We will forgo a law enforcement action in the furtherance of continuing to collect positive intelligence.

SHAPIRO: This is Michael Heimbach, assistant director for the bureau's counterterrorism division. He says when to act is always a subjective call. When there's a disagreement between investigators and prosecutors, and investigators think we really need to keep going with this investigation, but prosecutors think no, we need to take these guys off the street and indict them, who wins that?

MONTAGNE: I don't think there's any win or lose. I mean, it's a very collegial process where myself, my team, along with the Justice team, will converge, meet, discuss the pros and cons, and at the end of the day, we'll come up with a common solution of what's the best endgame here.

SHAPIRO: But people who have left the government and can now speak frankly say of course there are battles.

MONTAGNE: There were certainly times when you felt like you were at loggerheads.

SHAPIRO: David Deitch used to be a prosecutor in the Justice Department's counterterrorism section.

MONTAGNE: The federal agency that had classified the information in some ways held the cards.

SHAPIRO: That's the FBI, right?

MONTAGNE: Yes. By and large, when you're talking about FISA, it was usually talking about the FBI, and if that agency was unwilling to declassify the information, that could be a stumbling block and sometimes an insurmountable one to going forward with a prosecution.

SHAPIRO: As the balance shifts from prosecuting to investigating and back again, there are two opposing risks. One is that the FBI will watch people for too long, and terrorists will carry out a plot. The other is that prosecutors will bring charges too soon. They won't have a case, and they may miss a bigger plot.

Former prosecutor David Laufman believes at this point, the FBI is erring on the side of waiting too long.

MONTAGNE: There is a widely held frustration among counterterrorism agents in the FBI and many prosecutors that the pendulum has swung too far in favor of intelligence gathering.

MONTAGNE: That doesn't surprise me.

SHAPIRO: Former FBI official Michael Woods.

MONTAGNE: I think back to the 1990s, when there was a lot of frustration in the FBI intelligence circles about the pendulum swinging too far in the direction of prosecutions.

SHAPIRO: He says the pendulum keeps swinging, and half the people are always going to be unhappy. Ari Shapiro, NPR News, Washington.

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