Mueller said last week that he had "a fairly high level of confidence" that the FBI knew the real names of the hijackers, based on flight manifests and follow-up interviews.
But while in Pennsylvania on Thursday for a tour of the crash site there, he raised fresh doubts about the accuracy of the identifications.
"We have several hijackers whose identities were those of the names on the manifests," Mueller said. "We have several others that are still in question. The investigation is ongoing, and I am not certain as to several of the others."
Officials refused to say how many hijackers may have used false identities, but officials of the Saudi Arabian government said Thursday that six of the men that the United States has named as hijackers killed in the attacks appear to be living in the Middle East.
Investigators believe that some of the 19 suspected hijackers may have stolen the identities of law-abiding Middle Easterners, further complicating the probe.
Confusion over the identities of some of the terrorists is one reason authorities have delayed putting out the photographs of the hijackers, as they had planned to do last week, Justice Department spokeswoman Mindy Tucker said.
The Saudi citizens who were mistakenly linked to last week's tragedy are horrified, said a diplomat at the Saudi Embassy here.
"You should see the hate mail we are getting," said Gaafar Allagany, head of the embassy's information center. "We think this was part of the plan."
The six Saudis are:
* Abdulaziz Alomari, a name used by one of the suspected hijackers on American Airlines Flight 11, the first plane that crashed into the World Trade Center.
A man with the same name is an electrical engineer in Saudi Arabia. He lived in Denver, where he got his degree from the University of Colorado, from 1993 until last year.
"In 1995, his apartment was broken into in Denver and his passport and other official documents were stolen," Allagany said.
* Salem Alhamzi, a name used by one of the suspected hijackers on American Airlines Flight 77, the plane that crashed into the Pentagon.
A man with the same name works for the Saudi Royal Commission in the Saudi city of Yanbu.
* Saeed Alghamdi, a name used by one of the alleged hijackers on United Airlines Flight 93, the plane that crashed in Pennsylvania.
A Saudi Arabian pilot, currently on a mission to Tunisia, has the same name.
* Ahmed Alnami, a name used by another suspected hijacker on Flight 93.
A 33-year-old Saudi Arabian pilot with the same name is alive in Riyadh.
* Wail Alshehri, a name used by one of the suspected hijackers on American Airlines Flight 11.
A man by the same name is a pilot whose father is a Saudi diplomat in Bombay. "I personally talked to both father and son today," Allagany said.
* Waleed M. Alshehri, a name used by another alleged hijacker on Flight 11, is the same name as the other son of the diplomat. Allagany said that man is living in Jidda.
"This is a respectable family. I know his sons, and they're both alive," he said.
In other developments Thursday, an FBI official in San Antonio discounted any ties between two Indian nationals arrested on an Amtrak train in Fort Worth last week and a San Antonio physician also being held for questioning following the terror attacks.
"There's no connection" between them "at this time," said special agent Rene Salinas, spokesman for the FBI's office in San Antonio.
Salinas also said federal agents found nothing suspicious in the purchase of airline tickets from San Antonio to San Diego for a scheduled flight Saturday by the physician, Al-Badr Al-Hazmi. The 34-year-old Saudi national is studying at the University of Texas Health Science Center.
The FBI list of people wanted for questioning included Al-Hazmi and four other people, three with the surname Al-Hazmi. According to the list, the five individuals were booked on the same flights leaving Saturday from San Antonio, going to Denver and on to San Diego, and then returning Oct. 20.
Also Thursday, a Muslim cleric questioned by prosecutors about last week's attacks called the suicide operations "vicious and cowardly acts of terror" and also protested his treatment by the FBI.
The clergyman, Moataz Al-Hallak, led a mosque in suburban Dallas, where suspected terrorist Osama bin Laden's former personal secretary prayed.
"We had a calamity," Al-Hallak said. "We don't want to add more innocent victims. It's been hard."
Bin Laden's former secretary was convicted in May of conspiring to kill Americans in the 1998 bombings of U.S. embassies in Kenya and Tanzania. Al-Hallak testified three times under a grant of immunity to the grand jury in that case.
Thirteen months ago, Al-Hallak moved to a suburb of Washington, where the five hijackers suspected of forcing a plane into the Pentagon apparently spent the week before the crash.
FBI agents in Dallas told reporters last week that they wanted to speak to Al-Hallak in connection with the attacks. His name, native land and birth date were entered on the agency's watch list.
Agents said Al-Hallak may have made statements predicting the attacks while he was visiting Texas, an assertion his lawyer denied.
On Wednesday, the clergyman spent three hours with federal prosecutor Patrick Fitzgerald, who led the government's case in the embassy bombings trial. Al-Hallak said he answered every question.
"I don't know Bin Laden. I don't know what he did. I don't know what he did not do," Al-Hallak said at a Thursday news conference.
Bin Laden "has been accused of committing horrible crimes," Al-Hallak said. "These accusations need to be proved in a court of law, and justice needs to be established."
Given the confusion over suspects' identities, the FBI is moving carefully to determine whether a man arrested near Chicago late Wednesday--identified as Nabil Al-Marabh--is the man on a watch list of possible associates of the terrorists.
Kathleen McChesney of the Chicago FBI office said Al-Marabh's vehicle and residence were searched and that numerous law enforcement agencies, including a Chicago-based terrorism task force and the Immigration and Naturalization Service, are working together "so we know exactly who this person is."
Al-Marabh, a 34-year-old former cabdriver, was picked up in Burbank, Ill., at a convenience store where he had worked for several days.
Al-Marabh was being held on a warrant from Boston stemming from probation violations.
Property records indicate that in the mid-1990s he shared a Boston apartment with accused terrorist Raed Hijazi.
Hijazi is in jail in Jordan on charges that he planned to blow up a hotel during millennium celebrations. Both men drove taxis for the Boston Cab Co.
Federal officials believe Al-Marabh and Hijazi may have close ties to two of the suspected hijackers in last week's attack. They also have been linked with two men suspected of helping to plan last year's bombing of the U.S. destroyer Cole in Yemen.
Authorities last week scoured a series of residences in Boston where Al-Marabh lived over 10 years. On Monday, federal agents raided a Detroit residence with his name on the mailbox.
According to law enforcement documents, Al-Marabh was three hours away from Detroit at the time, obtaining a driver's license in Three Oaks, Mich., near the Indiana border.
Al-Marabh, a short, stocky native of Kuwait, pleaded guilty in Boston last December to stabbing his roommate. Witnesses said he yelled, "If this wasn't America, I'd kill you."
His court-appointed lawyer, Robert Menton, said Al-Marabh told him he stabbed Arafat Abuhejeb "because he deserved it." Menton said his client described himself as a holy man with a degree in international relations from a Middle Eastern university. He also told his lawyer he had a wife at home in Kuwait.
But Al-Marabh told at least one of his numerous Boston-area landlords that the Vietnamese woman he lived with was his wife.
Although a court file called him an indigent, Al-Marabh "always seemed to have money" and traveled often, his lawyer said. Menton said his client was concerned about being sentenced to jail for the stabbing "because he said he needed to get back to Kuwait."
He was given a six-month suspended sentence. But probation department records in Boston show that he never reported, as he was ordered to do, and an arrest warrant was issued for him in March.
In addition, records from the office of the Michigan secretary of state show that on Sept. 11, 2000, Al-Marabh obtained a license that permits him to drive semi-trucks containing hazardous materials, including explosives and caustic materials.
Times staff writers Ken Ellingwood, Scott Glover, Greg Krikorian, Matt Lait, H.G. Reza and Eric Lichtblau and researcher John Beckham contributed to this report.