Still, critics of Justice Department anti-terrorism policies say the study lifts the veil on what they consider to be large-scale government deception aimed at reassuring an American public fearful of more attacks.
"This punches a huge hole in the hype the Justice Department has been engaged in," said Timothy Edgar, legislative counsel for the American Civil Liberties Union.
"They are calling people terrorists, on a massive scale, who aren't terrorists," he said.
According to the study, charges were filed against 2,001 of the 6,400 people recommended for prosecution since the attacks. Authorities declined to prosecute 1,554. Some 2,845 of the referrals were pending as of Sept. 30.
Of the 879 people convicted, 373 went to prison and 506 did not. Of those sentenced to prison, 250 got less than a year, 100 got less than five years and just 23 were sentenced to five years or more.
During the two years before Sept. 11, 2001, 24 people were sentenced to five or more years in prison on comparable terror-related offenses, the study said.
The study found that prosecutions of individuals suspected of ties to one category, international terrorism, jumped from 142 in the two years before Sept. 11, 2001, to 748 in the two years after. Yet only three people in that category since the attacks have drawn sentences of five years or more, compared with six during the earlier period.
It also showed that more than 260 people convicted since September 11 of terrorism-related offenses were sentenced to the time that had already spent in jail awaiting disposition of their case.
Finally, the study said that 35 percent of criminal referrals made by investigators were declined by prosecutors because of lack of evidence or because no obvious federal crime had been committed.
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