Agent Harry Samit testified under cross-examination at Moussaoui's trial that FBI headquarters' refusal to follow up "prevented a serious opportunity to stop the 9/11 attacks" that killed nearly 3,000 people.
Moussaoui is the only person charged in this country in the attacks.
The FBI's actions between Moussaoui's arrest on immigration violations on Aug. 16, 2001, and Sept. 11, 2001, are crucial to his trial because prosecutors allege that Moussaoui's lies prevented the FBI from thwarting or at least minimizing the Sept. 11 attacks. Prosecutors must prove that Moussaoui's actions caused the death of at least one person on 9/11 to obtain a death penalty.
But CBS News correspondent Jim Stewart reports that analysts, as well as Samit's testimony, suggest the FBI had enough trouble connecting dots even if Moussaoui admitted being an al Qaeda terrorist.
Under cross-examination by defense attorney Edward MacMahon, Samit acknowledged that he warned higher-ups and others in the government at least 70 times that Moussaoui was a terrorist, CBS News correspondent Barry Bagnato reports.
He said he sought Justice Department permission to seek a search warrant — and never got it.
"You needed people in Washington to help you out?" MacMahon asked.
"Yes," Samit said.
"They didn't do that, did they?"
Samit said no.
He confirmed under questioning that he had attributed FBI inaction to "obstructionism, criminal negligence and careerism" in an earlier report.
One FBI supervisor in Washington told Samit that he was getting unnecessarily "spun up" about his concerns over Moussaoui.
Moussaoui pleaded guilty in April to conspiring with al Qaeda to hijack aircraft and commit other crimes. The sentencing trial will determine his punishment: death or life in prison.
Moussaoui denies he had anything to do with 9/11 and says he was training for a future attack.
MacMahon also questioned Samit on whether the government could have legally searched Moussaoui's Minnesota hotel room without first obtaining a warrant.
Samit said that in certain circumstances agents can conduct a search on foreign nationals immediately and obtain a warrant after the fact. But he said in Moussaoui's case, he and his supervisors determined that it would be best to arrest Moussaoui first.
Samit testified before the trial's recess last week that Moussaoui lied to him after his arrest and thwarted his ability to obtain a search warrant. Samit said that the FBI would have launched an all-out investigation if it had been able to search Moussaoui's belongings.
"You blew an opportunity to search ... without arresting him?" MacMahon asked Samit.
Samit responded, "That's totally false."
He said he found himself in a bureaucratic bind because he had opened an intelligence investigation on Moussaoui rather than a criminal investigation and therefore needed Justice Department approval to get a search warrant. Many of the barriers between criminal and intelligence investigations were removed after 9/11.
Samit's testimony comes a week after U.S. District Judge Leonie Brinkema delayed the trial because of a government blunder. It was a mistake that could have led to the judge giving Moussaoui life rather than death.
Transportation Security Administration attorney Carla Martin had improperly coached six witnesses who were to testify about aviation related events. Their testimony was viewed as crucial and represented about half the government's case.
The judge ruled those witnesses cannot testify, but others, not coached, can take the stand.
CBS News correspondent Drew Levinson reports Martin is ready to tell her side of the story, and may have to before the additional witnesses can state the stand.