Minneapolis FBI agents investigating terror suspect Zacarias Moussaoui last August were severely hampered by officials at FBI headquarters, who resisted seeking search warrants and admonished agents for seeking help from the CIA, according to a letter from the general counsel for the FBI's Minneapolis field office.

Coleen Rowley also wrote in a letter Tuesday to FBI Director Robert S. Mueller III that evidence gathered in the Moussaoui case, combined with a July 10 FBI warning that al Qaeda operatives might be taking flight training in Arizona, should have prompted stronger suspicion at FBI headquarters that a terror attack was planned, according to officials familiar with Rowley's letter.

"There was a great deal of frustration expressed on the part of the Minneapolis office toward what they viewed as a less than aggressive attitude from headquarters," said one official. "The bottom line is that headquarters was the problem."

The sharply worded letter from Rowley stands in stark contrast to statements by Mueller and other FBI officials, who have insisted that the bureau did all it could to determine whether Moussaoui was part of a terrorist plot. It is also the clearest sign of dissent within the FBI over whether the bureau mishandled clues to the Sept. 11 attacks last summer, an issue that has mushroomed this month amid increasingly fierce questioning from lawmakers.

Mueller released a statement last night saying that he has referred Rowley's complaints to the Justice Department's inspector general for investigation.

"While I cannot comment on the specifics of the letter, I am convinced that a different approach is required," Mueller said. "New strategies, new analytical capacities and a different culture makes us an agency that is changing post-9/11. There is no room after the attacks for the types of problems and attitudes that could inhibit our efforts."

In her classified 13-page letter, which includes detailed footnotes, Rowley said Minneapolis investigators had significant evidence of Moussaoui's possible ties to terrorists, including corroboration from a foreign source that Moussaoui posed a major threat, sources said.

But agent Dave Rapp and his colleagues in Minnesota faced resistance from headquarters staff that Rowley considered unnecessary and counterproductive, according to officials who have seen the letter.

FBI attorneys in Washington determined there was not enough evidence to ask a judge for warrants to search Moussaoui's computer under routine criminal procedures or a special law aimed at terrorists. Officials have said there was no evidence of a crime and no solid connections between Moussaoui and any designated terrorist group.

Moussaoui, who was detained Aug. 16 after arousing suspicions at a Minnesota flight school, has been charged as a conspirator in the Sept. 11 attacks on the World Trade Center and the Pentagon.

Mueller, who took over as FBI director on Sept. 4, was questioned about the letter during an appearance Wednesday before the Senate Intelligence Committee, sources said. One official said Mueller "was very forthright in saying the course of action should have been more aggressive."

Rowley, who officials said has worked for the FBI for more than 20 years, declined to comment yesterday. "Our office has been very diligent in not leaking anything," Rowley said. "I'm going to have to stick with that in this case."

In Berlin yesterday, President Bush said he opposed having an independent commission investigate intelligence failures before the Sept. 11 attacks. The House and Senate intelligence committees are currently conducting a probe.

More than a month before Moussaoui was arrested on immigration charges, Phoenix FBI agent Kenneth Williams wrote a memo July 10 to FBI headquarters outlining his investigation of Islamic radicals enrolled at a Prescott, Ariz., aviation school. He cited bin Laden and raised the possibility that the al Qaeda terror network was using U.S. flight schools as a training ground.

Williams's suggestion that the FBI canvass U.S. flight schools was rejected within weeks by FBI counter-terror division mid-level managers, who decided they lacked the manpower to pursue it. The memo was not shared with agents who later investigated Moussaoui, and it was never given to any other intelligence agency.

Williams told lawmakers in closed-door briefings this week, however, that he did not expect his request to be acted on immediately and did not believe his memo could have thwarted the Sept. 11 attacks. None of the men named in the document, including several associated with a militant London group that has praised bin Laden, has been connected to the deadly hijackings.

Rowley's correspondence, by contrast, underscores the depth of frustration within the Minneapolis field office over the way the Moussaoui case was handled.

"It really paints a very grim and troubling picture about the institution of the FBI at the end of August last year and how many obstacles the Minnesota office ran into," said one official familiar with the letter's contents. "Clearly she feels this was handled very poorly."

At one point, according to accounts of Rowley's letter, agents in Minnesota went to the CIA for help, only to be admonished by headquarters.

The FBI first notified the CIA about Moussaoui soon after arresting him, a U.S. government official said. The CIA found nothing in an initial check of Moussaoui's name, but over the next couple of weeks, French intelligence interviewed Moussaoui's brother and the parents of a man who blamed Moussaoui for radicalizing their son, according to U.S. sources, and turned over the information.

In late August, CIA officials learned from "FBI agents in the field" that they hoped to obtain a warrant under the Foreign Intelligence Surveillance Act, which would have allowed the government to search Moussaoui's laptop computer without notifying him, one government official said. He could not confirm that this was the contact that brought the admonishment.

The hard drive of Moussaoui's computer, which was finally searched several hours after the Sept. 11 attacks, was found to include detailed information on crop-dusting and on the type of jetliner hijacked. The computer also included the names of Moussaoui associates in Singapore and elsewhere that could have opened new paths for investigators, two sources said.

"The argument is that there was already probable cause and headquarters didn't move aggressively enough," one source said. "If you had the analysis from Phoenix, that would have made the case even better."

Two officials who have read the letter said Rowley indicated she was upset by Mueller's public statements about the extent of the FBI's knowledge before Sept. 11.

In testimony earlier this month before the Senate Judiciary Committee, Mueller acknowledged that the FBI should have responded more aggressively to the Phoenix memorandum, but he argued that the FBI did all it could in pursuing Moussaoui.

"The agent in Minneapolis did a terrific job in pushing as hard as he could to do everything we possibly could with Moussaoui," Mueller said. "But did we discern from that that there was a plot that would have led us to September 11th? No. Could we have? I rather doubt it."

Staff writer Dana Milbank in Berlin contributed to this report.