The FBI challenged the methodology of the analysis, saying it led to "misleading and unfounded conclusions ..."
The analysis, carried out by statisticians and long-time law enforcement observers at the Transactional Records Access Clearinghouse based at Syracuse University, found that in the two years after the Sept. 11 attacks about 6,400 people were referred to prosecutors in connection with terrorism or terrorist offenses.
But of the 2,681 cases that had been wrapped up by the end of September 2003, some 879 were convicted of a crime and less than half of those -- 373 -- were sent to prison. Five received sentences of 20 years or more, which was actually fewer than in the two years before Sept. 11.
The figures analyzed have been repeatedly cited by administration officials to justify their contention that the government is winning the war against terror.
"Our report raises serious questions," David Burnham of TRAC told United Press International, "When such large numbers of cases are declined, dismissed or acquitted, we have to ask: Is the government pursuing the right strategy (in the war on terror)? Are they targeting the right people?"
Burnham pointed out that nearly half the cases sent to federal attorneys were never prosecuted at all. "What does this say about the quality of the investigators?" he asked.
"This report underscores concerns that I and others have raised," said Sen. Patrick Leahy, D-Vt., in a statement. He said that he had written to officials earlier this year when the justice department first made the figures available, but had not received a response.
The American Civil Liberties Union said the report "punctures the hype that the Justice Department and government have used to justify the Patriot Act and other measures they say are need to fight terrorism."
But the FBI, in a statement issued Sunday, said the report's data was "taken out of context," because the authors used the terms "referred to prosecutors" and "recommended for prosecution" interchangeably.
In fact, FBI spokesman Jim Parsell told UPI it was an administrative requirement for every case investigated to be referred to prosecutors so it could be closed, even when there was no prospect of a successful prosecution. The result of these flaws, said the FBI, was a "misleading and unfounded conclusion about federal law enforcement."
The report authors acknowledge that hundreds of cases included in their overall total of 6,400 were still pending at the time of their analysis, and that -- since more serious cases tend to be more complex and take longer to complete -- the numbers receiving long sentences was likely to rise as time went on.
Indeed, since the Sept.30, 2003, cut-off date for TRAC's data, at least four men -- two members of the so-called Lackawanna Six from upstate New York, and two from Oregon -- have been sentenced to more than five years in prison for terrorist crimes.
Tim Edgar of the ACLU told UPI that the data showed the government was "cooking the books" on the war against terror.
In a speech at the FBI academy in Quantico, Va., on Sept. 10, President Bush -- ticking off a long list of continuing achievements in the war on terror -- said, "More than 260 suspected terrorists have been charged in U.S. courts; more than 140 have already been convicted."
"This report reveals the gap between that rhetoric and the reality," said Edgar.
"These figures have been used over and over again by the president and others to make people feel safer and to stifle the debate about whether the administration's strategy and the new laws they've passed are working."
Department of Justice spokesman Mark Corallo released a statement citing the case of Al Capone, a notorious gangster of the prohibition era, who was eventually imprisoned for income tax evasion.
"Today," Corallo's statement went on, "in order to protect the lives of Americans ... the government may charge potential terror suspects with lesser offenses to remove them from our communities."
But even with these convictions -- referred to by the department as "anti-terrorism cases" -- factored out, less than half of those convicted were sent to jail.
The FBI said that this was because the figures included sentences for some relatively minor offenses, such as identity fraud, or failing to register as the agent of a foreign government.
Edgar said that this kind of classification was "prosecutorial abuse."
"The Justice Department has labeled more than 6,000 people terrorists," he said but the sentencing figures told a different story.
At the sentencing stage of any trial, he explained, the prosecution is entitled to introduce evidence about the defendant unrelated to the case, and the court can take it into account even if it is not proved beyond a reasonable doubt.
"We see the Justice Department doing this," said Edgar, "but, as the figures show, the judges aren't buying it."
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