The department's office of inspector general, which investigates waste, fraud and abuse, also is looking into allegations that senior FBI officials are immune from disciplinary measures and punishments imposed on lower-ranking agents.
Agents have complained to lawmakers of a double standard at the bureau, as evidenced by top managers not being held accountable while they often place blame for bureau blunders on subordinates.
Department spokeswoman Mindy Tucker said Inspector General Glen Fine began his investigation in May.
The FBI is under intense scrutiny after a string of mishaps. Fine is conducting three other investigations of the agency on the case of Robert Hanssen, a veteran agent who confessed to spying for Russia; on the belated discovery of Oklahoma City bombing documents; and on the loss by the bureau of weapons and laptop computers.
The incident at Ruby Ridge, Idaho, pitted FBI agents against white separatist Randy Weaver and led to the deaths of a deputy U.S. marshal, Weaver's wife and a teen-age son.
A federal appeals court ruled this year the agents were acting under rules of engagement that "are patently unconstitutional for a police action." The court ruled that an FBI sniper could be charged with criminal manslaughter in the standoff, but Idaho prosecutors decided not to press charges.
FBI agent John Roberts and two other agents assigned to investigate the bureau's handling of the siege have said they received threats and retaliation from superiors. Roberts said a supervisor began "to take out his anger on my wife," an FBI support employee.
The Justice Department's Office of Professional Responsibility recommended sanctions against FBI Director Louis Freeh and other senior officials. Freeh was not FBI director at the time of the standoff, but he headed the bureau during an internal investigation afterward.
Last January a top Justice Department official decided against censuring Freeh and the others. Lawmakers, who only recently learned of the decision, said it was evidence of a "good-old-boy" network at the agency.
As part of examining whether a double standard exists in the bureau, the inspector general will look at the decision, made by former Assistant Attorney General Stephen Colgate, Tucker said.
The investigation was reported Thursday in The Washington Post.
Freeh retired from the FBI in June, two years short of his 10-year tenure.
Robert Mueller, a veteran federal prosecutor who ran the Justice Department's criminal division during the previous Bush administration, was confirmed last week as FBI director.
By KAREN GULLO
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