By DAVID JOHNSTON WASHINGTON, Aug. 13 — The Justice Department today made public two chapters of a classified internal inquiry that harshly criticized the investigation of the Los Alamos nuclear scientist Wen Ho Lee. The report faulted the Energy Department as producing a deeply flawed preliminary report and the F.B.I. as conducting an inadequate investigation into accusations that Dr. Lee had mishandled nuclear weapons data. The existence of the report has long been known, along with its generally critical commentary on the Wen Ho Lee case. But the chapters released today, which were heavily edited to delete references to material that remains classified, show how the government's own post-mortem harshly criticized the Lee inquiry over faulty assumptions, slipshod methods and an unwillingness to look beyond Dr. Lee to other suspects. The undated report, written more than a year ago by Randy I. Bellows, a veteran federal prosecutor in Virginia, said that an administrative inquiry used by the Energy Department as the basis for recommending an F.B.I. investigation of Dr. Lee, was "a deeply flawed product whose shortcomings went unrecognized and unaddressed due to the F.B.I.'s own inadequate investigation." Critics had accused investigators of singling out Dr. Lee because of his Chinese ancestry. Senator Patrick J. Leahy, a Vermont Democrat and chairman of the Judiciary Committee, said today that the report indicated that the Lee investigation was mismanaged. "The report paints the picture of a wayward investigation that was flawed from inception," Mr. Leahy said. "It provides newly public details of communications breakdowns, flawed assessments and inaccurate representations that for years misdirected the Department of Energy's administrative inquiry and the later F.B.I. investigation," Mr. Leahy said. "Even if not racially motivated, the abysmal handling of the initial phases of this case caused serious harm and delay in resolving fundamental questions about a grave compromise of our nuclear secrets." The report found that the Energy Department and then the Federal Bureau of Investigation mistakenly narrowed their investigation to Dr. Lee as a suspect in the possible, but unproven, theft of nuclear secrets. The report concluded that the F.B.I. accepted the department's conclusions about Dr. Lee without a rigorous examination of the agency's rationale, or predicate, for suspecting him. "But to say that D.O.E. misled the F.B.I. as to the predicate and to say that D.O.E. improperly focused its conclusion only on Wen Ho Lee is only to describe half the problem," the report said. "The other half was the F.B.I.'s unfortunate and unwarranted acceptance of D.O.E.'s description of the predicate, its unhesitating and unquestioning acceptance of D.O.E.'s identification of Lee as `the most logical suspect,' " the report said. The case against Dr. Lee collapsed in September 2000 when the government dropped all but one of the 59 felony charges against him. He pleaded guilty to a single count of mishandling nuclear secrets, and the case became an embarrassment for the F.B.I., which conducted the criminal inquiry that led to the criminal charges against him. The chapters were disclosed under orders of Magistrate Judge Thomas R. Jones Jr. in Alexandria, Va., as part of a defamation lawsuit filed by Notra Trulock, the Energy Department's former chief of counterintelligence. Mr. Trulock has sued Dr. Lee and two Energy Department investigators who, Mr. Trulock said, had wrongly accused him of singling out Dr. Lee for investigation because of his Chinese ancestry. The Bellows report said a full inquiry of Mr. Lee was warranted, but concluded that the Energy Department's own administrative report focused on Dr. Lee, a Taiwanese-born, naturalized citizen, without considering other suspects who had access to the same highly secret W-88 warhead design information that Dr. Lee was suspected of compromising. No one else was ever subjected to similar scrutiny. Mr. Bellows's report concluded: "The final report was so poorly written and organized that this alone made it difficult to evaluate and comprehend. More significantly, it contained very serious deficiencies, including numerous inconsistent and contradictory statements as well as unsubstantiated assertions." But the report "found no evidence of racial bias" and Mr. Bellows rejected complaints by some officials that the initial Energy Department review was little more than "a mechanism to summarily finger a Chinese American." The chapters released today are only a small part of the report, law enforcement officials said. They said the remainder would be made public in several weeks. Copyright 2001 The New York Times Company