In one instance, someone altered dates on three F.B.I. forms using correction fluid to conceal an apparent violation of federal wiretap law, according to a draft report of an investigation by the Justice Department inspector general's office obtained by The New York Times. But investigators were unable to determine who altered the documents.

The agent who first alerted the F.B.I. to problems in the case, a veteran undercover operative named Mike German, was "retaliated against" by his boss, who was angered by the agent's complaints and stopped using him for prestigious assignments in training new undercover agents, the draft report concluded.

Mr. German's case first became public last year, as he emerged as the latest in a string of whistle-blowers at the bureau who said they had been punished and effectively silenced for voicing concerns about the handling of terror investigations and other matters since Sept. 11, 2001.

The inspector general's draft report, dated Nov. 15 and awaiting final review, validated most of Mr. German's central accusations in the case. But the former agent, who left the bureau last year after he said his career had been derailed by the Florida episode, said he felt more disappointment than vindication.

"More than anything else, I'm saddened by all this," Mr. German said in an interview. "I still love the F.B.I., and I know that there are good, honest, hard-working agents out there trying to do the right thing, and this hurts all of them."

Robert S. Mueller III, director of the F.B.I., has emphasized repeatedly, both publicly and in private messages to his staff, that employees are encouraged to come forward with reports of wrongdoing and that he will not tolerate retaliation against whistle-blowers.

Senator Charles E. Grassley, an Iowa Republican who has been a frequent critic of the bureau, said of Mr. German: "Unfortunately, this is just another case in a long line of F.B.I. whistle-blowers who have had their careers derailed because the F.B.I. couldn't tolerate criticism."

Michael Kortan, an F.B.I. spokesman, said the bureau had not been briefed on the findings. But Mr. Kortan said that when the F.B.I. received the report, "if either misconduct or other wrongdoing is found, we will take appropriate action."

Ann Beeson, associate legal director for the American Civil Liberties Union, said that the inspector general's findings, coming just days after the Supreme Court refused to hear an appeal from an earlier F.B.I. whistle-blower, pointed to the need for tougher measures to protect those who report abuse. "With courts reluctant to protect whistle-blowers, it is crucial that Congress pass additional protections," Ms. Beeson said.

Mr. German's case dates to 2002, when the F.B.I. division in Tampa opened a terror investigation into a lead that laundered proceeds, possibly connected to a drug outfit, might be used to finance terrorists overseas. The F.B.I. was considering initiating an undercover operation to follow the lead, and Mr. German, who had extensive experience infiltrating militias, skinheads and other groups, was asked to take part.

But in the coming months, Mr. German would alert F.B.I. officials that the Orlando agent handling the case had "so seriously mishandled" the investigation that a prime opportunity to expose a terrorist financing plot had been wasted. He said agents had not adequately pursued leads, had failed to document important meetings with informants, and had tolerated violations of rules and federal law on the handling of wiretaps.

The report, in one of its few dissents from Mr. German's accusations, said it could not confirm that the F.B.I. had missed an important chance to expose terrorism. Rather, it cited two findings by the bureau that the prime informant had misled agents about the terrorism angle in the case and that "there was no viable terrorism case."

Nonetheless, the inspector general found that the F.B.I. had "mishandled and mismanaged" the investigation, partly through the failure to document important developments for months at a time. The report also found that supervisors were aware of problems in the case but did not take prompt action to correct them.

Moreover, after Mr. German raised concerns about the lack of documentation, an unnamed agent in Orlando "improperly added inaccurate dates to the investigative reports in order to make it appear as though the reports were prepared earlier," the inspector general found.

In addition, someone used correction fluid to backdate by two months a set of forms that the main informant had signed as part of a bugging operation, in which he agreed that he had to be present for all undercover taping.

The backdating was significant, the inspector general said, because the informant had taped a 2002 meeting with several suspects but had left the recording device unattended while he went to use the restroom - a violation of federal law.

Mr. German became increasingly vocal within the F.B.I. about what he saw as the bureau's failure to correct missteps, taking his concerns directly to Mr. Mueller in a 2003 e-mail message. His complaints, the inspector general found, led agents in Florida, Washington and Oregon to distance themselves from him.

In the most serious instance, the head of the F.B.I. undercover unit, Jorge Martinez, froze Mr. German out of teaching assignments in undercover training and told one agent that Mr. German would "never work another undercover case," the report said.

Mr. Martinez told investigators that he did not remember making the statements but that if he had, it was a "knee-jerk reaction but did not mean to indicate I was retaliating against him," the report said.

The inspector general disagreed. It said in the report that Mr. Martinez's treatment of Mr. German amounted to improper retaliation and "discrimination that could have a chilling effect on whistle-blowing."