Faced with a highly critical report, FBI Director Robert Mueller (search) on Friday promised changes in the handling of illegal immigrants suspected of having links to terrorism.

In a speech to an American Civil Liberties Union (search) conference, Mueller said the report last week from the Justice Department's inspector general "did a very good job of pointing out areas where we can do better."

The inspector general, Glenn A. Fine, criticized the lengthy detentions — some up to eight months — of many of the 762 aliens held in the aftermath of the Sept. 11 terror attacks and the FBI's assumption of sole authority to decide whether individuals remained a threat.

Conditions of custody were often unduly harsh and none of the detainees were convicted of terrorism-related offenses, with such charges brought only against Zacarias Moussaoui (search).

Among the changes, Mueller said, are better criteria for deciding when an illegal alien is a suspect of special concern, improved communication between agencies to accelerate the disposition of the cases and more personnel devoted to the investigations.

In addition, federal immigration officials will have greater authority over custody of these illegal aliens, with the FBI taking over only if the case is made in writing that release of an individual poses a threat or would disrupt an investigation.

Assistant Attorney General Michael Chertoff, head of the Justice Department's criminal division, said in a recent letter to the Senate Judiciary Committee that the FBI and Homeland Security Department — which now handles most immigration matters — are working to implement these changes.

"These enhancements would further reduce the potential for impinging on civil liberties," Chertoff said in the June 4 letter, which he said stated his personal views and not official government policy. Chertoff leaves his post Monday to become a judge on the 3rd U.S. Circuit Court of Appeals.

The fate of Sept. 11 detainees was only one of the issues that has drawn criticism from the ACLU in the war against terrorism. The ACLU has repeatedly fought against government secrecy, questioned the increased surveillance powers under the USA Patriot Act (search) and raised concern that the FBI singles out Muslims for investigation after the attacks.

ACLU Executive Director Anthony Romero praised Mueller for his willingness to appear before such a critical crowd, albeit one that received him warmly. But Romero added that "the areas of disagreement outnumber the areas of agreement" between his group and the FBI.

Mueller said the FBI had redoubled its dedication to upholding citizens' rights under the Constitution, although is still its top priority. Some secrecy is necessary in combating terror, he said, but many concerns about infringement of rights have been overblown.

For instance, Mueller said the FBI has only investigated patrons' use of library books and computers when probing specific individuals with court-approved warrants, rather than using random sweeps that critics fear.

"The FBI will be judged not just on how we effectively disrupt and deter terrorism, but also on how on how we protect the civil liberties and constitutional rights of all Americans," Mueller said. "We must accomplish both, so that future generations can enjoy lives that are both safe and free."