(CBS) Concerned that Washington headquarters was hindering their pre-Sept. 11 probe of terrorism defendant Zacarias Moussaoui, FBI agents in Minnesota took the radical step of contacting the CIA for help, an FBI whistleblower says.

Agent Coleen Rowley took the rare course this week of sending her allegations directly to the head of the FBI, Robert Mueller. Copies were sent to members of the Senate Intelligence Committee.

"The bottom line is that headquarters was the problem," an unnamed official told the Washington Post in Friday's editions.

Mueller on Thursday ordered an internal inspector general's investigation of Rowley's allegations. A House-Senate committee added her charges to its investigation of intelligence failures leading up to the Sept. 11 attacks.

The classified letter surfaced a day after the Senate Intelligence Committee questioned Mueller about it in a closed session. It marked the first known time that any of the FBI's own agents have formally complained about the bureau's failure to pursue aggressively potential warnings before Sept. 11.

Rowley's 13-page letter, which accused FBI headquarters of erecting a “roadblock” to the Moussaoui investigation, was delivered Tuesday. A Senate source, speaking only on condition of anonymity, said she was interviewed by congressional investigators Wednesday.

After the Minnesota agents violated agency protocol by going to the CIA, they were reprimanded, Rowley said.

“When, in a desperate 11th-hour measure to bypass the FBI HQ roadblock, the Minneapolis division undertook to directly notify the CIA's counterterrorist center, FBI HQ personnel chastised the Minneapolis agents for making the direct notification without their approval,” she wrote.

The allegations surfaced hours after President Bush said he wanted congressional intelligence committees, not a special commission, to investigate how the government dealt with terror warnings before Sept. 11.

After receiving Rowley's letter, Mueller acknowledged his agency needed a “different approach” to fighting terrorism.

In November, the FBI director wrote a memo to all employees that promised protection for whistleblowers.

“I will not tolerate reprisals or intimidation by any bureau employee against those who make protected disclosures, nor will I tolerate attempts to prevent employees from making such disclosures,” he wrote.

Moussaoui, a French citizen of Moroccan descent, is the only person charged as an accomplice with Osama bin Laden and the 19 hijackers in the Sept. 11 suicide hijackings. He was arrested a month before the attacks after arousing suspicions with his flight training.

Government officials confirmed Thursday night that the CIA received at least two pre-Sept. 11 contacts from the FBI concerning Moussaoui.

In mid-August, the FBI told the CIA of concerns Moussaoui might be a terrorist, and the CIA checked its own files and found nothing on him. The CIA also made a routine request from foreign governments that yielded intelligence from France that Moussaoui was a known Islamic extremist, the officials said.

The second contact came in late August when FBI agents in Minnesota told CIA officers they were seeking a warrant on Moussaoui, the official said.

Government officials familiar with Rowley's letter, who spoke on condition of anonymity, said the agent asserted that FBI headquarters did not fully appreciate the terrorist threat Moussaoui posed and hindered local agent's efforts to get warrants to gather more evidence.

“The agents in Minneapolis who were closest to the action, and in the best position to gauge the situation locally, did fully appreciate the terrorist risk/danger posed by Moussaoui and the possible co-conspirators even prior to Sept. 11,” Rowley wrote.

Mueller said in his statement, “I am convinced that a different approach is required. New strategies, new technologies, new analytical capacities and a different culture makes us an agency that is changing post-Sept. 11.

“There is no room after the attacks for the types of problems and attitudes that could inhibit our efforts.”

Sen. Charles Grassley, R-Iowa, a critic of the FBI and a strong defender of whistleblowers, said he was shocked but not surprised by Rowley's allegations.

Sen. John McCain, R-Ariz., co-sponsor of legislation for an independent investigation, said the problems the Minnesota office experienced were “not an intelligence failure per se. It's the way the FBI works.”

Officials familiar with Rowley's allegations said the agent claimed the bureau made a series of mistakes last summer when agents became suspicious of Moussaoui and arrested him after he wanted training on a 747 simulator at a Minnesota flight school.

The officials, who spoke on condition of anonymity, said some of the allegations involve how the bureau handled efforts to get a special national security warrant and a regular search warrant to gather evidence against Moussaoui.

Law enforcement officials have said previously that information that came into law enforcement before Sept. 11 included intelligence from France suggesting Moussaoui had terrorist ties and had been placed on a watch list in 1999.

But the information was insufficient to show he was an agent of a foreign power and eligible to be monitored under a national security warrant, officials have said.

After Sept. 11, FBI agents found evidence on Moussaoui's computer and elsewhere that linked him to the hijacking plot, according to court documents.

In another development, the House worked into the night on a $29 billion anti-terrorism bill. The Senate, a target of an anthrax attack last year, sent President Bush a broad bioterrorism measure. It would provide $4.6 billion to stockpile vaccines, improve food inspections and boost security for water systems.