Documents filed by federal lawyers in a Florida lawsuit appeared to contradict the government in its case against accused anthrax killer Bruce Ivins.

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WASHINGTON — Since it began a decade ago, the federal government’s investigation of the 2001 anthrax attacks has been plagued by missteps and complications.

Investigators initially focused on the wrong man and then had to pay him a nearly $6 million settlement. In 2008, they accused another man, Bruce Ivins, who killed himself before he could go to trial.

In the latest twist, the government is arguing against itself.

In the files of a recently settled Florida lawsuit, Justice Department civil attorneys contradicted their department’s conclusion Ivins was unquestionably the anthrax killer. The lawyers said the type of anthrax in Ivins’ lab was “radically different” from the deadly anthrax. They cited several witnesses who said Ivins was innocent, and they suggested a private laboratory in Ohio could have been involved in the attacks.

The unusual spectacle of one arm of the Justice Department publicly questioning another has the potential to undermine one of the most high-profile investigations in years, according to critics and independent experts who reviewed the court filings.

“I cannot think of another case in which the government has done such an egregious about-face. It destroys confidence in the criminal findings,” said Paul Rothstein, a law professor at Georgetown University.

The documents were filed in a lawsuit over the October 2001 death of Robert Stevens, a Florida photo editor who was the first victim of the attacks. His survivors accused the government of negligence for experimenting with anthrax at Fort Detrick, Md., a case that lingered in court until the Justice Department quietly settled it in late November.

Glimpse inside

The case, Stevens v. United States, offers a rare glimpse inside a typically unified and notoriously tight-lipped agency. Justice Department prosecutors and FBI officials said they stand behind their conclusions that Ivins prepared and mailed the anthrax-laced letters, which killed five people and terrified the nation just after Sept. 11, 2001. They said the civil filings were legal hypotheticals designed to shield the government from a negligence lawsuit filed by the family of an anthrax victim.

Yet last summer, when criminal investigators learned their conclusions had apparently been challenged — by their colleagues — they were surprised and frustrated, leading to shouting matches within the department before it rushed to change portions of the filings, according to people familiar with the events.

Experts said the civil lawyers went beyond the typical arguments attorneys make to avoid government liability, especially in a situation in which the Justice Department’s criminal side had already accused Ivins.

“When there have been so many public statements about Ivins’ guilt, someone higher up in the department should have seen this collision coming down the tracks,” Rothstein said.

Critics said the confusion has raised new doubts about the already disputed criminal investigation of Ivins. The Fort Detrick scientist committed suicide in 2008 as investigators were closing in on him, and the Justice Department closed the case in 2010.

The Stevens case documents “should put a gun to the case and explode it,” said Meryl Nass, a physician who — along with many of Ivins’ colleagues and some members of Congress — has long questioned his guilt.

“Reasonable doubts”

Paul Kemp, a lawyer for Ivins, said the civil lawsuit creates “not just reasonable doubt” about Ivins’ guilt but “millions of reasonable doubts.”

Justice Department and FBI officials countered that the evidence remains overwhelming Ivins alone sent the spore-laden letters to news media and two U.S. Senate offices, also sickening 17 people. The department did not provide civil-division lawyers to comment on the case.

Department officials acknowledged the civil filings appeared contradictory but attributed this to imprecise wording, some of which was corrected, and they said the civil attorneys were just doing their jobs.

“Whatever we say, there’s always going to be some percent of the public that will say Ivins didn’t do this,” said Rachel Lieber, an assistant U.S. attorney.

Questions over lab

In defending the government against the Stevens lawsuit, civil lawyers tried to create distance between the Army lab where Ivins worked and the killer anthrax.

The lawyers wrote that the lab lacked the specialized equipment required to prepare the killer anthrax, a statement the Justice Department later retracted. They also cited a scientific report that had questioned the FBI’s key conclusion linking Ivins’ flask of anthrax spores to the attacks.

That conflicted with the department’s criminal side, which had linked Ivins, his lab and the deadly anthrax. The FBI had suggested Ivins prepared the killer spores in the lab, pointing to the anthrax he maintained there, sophisticated equipment in the facility and his unusual late-night hours around the time of the attacks.

After the documents were filed publicly, the civil attorneys, who had not checked beforehand with the FBI or U.S. Attorney’s Office, “got scolded, and rightly so,” said one person familiar with the events, who spoke on condition of anonymity.

Richard Schuler, an attorney for the Stevens family, said “there’s no question” the government’s decision to avoid a trial in the civil case was related to the conflicting evidence.

The Justice Department initiated settlement discussions in August, about a month after filing its motions, according to people familiar with the discussions. The settlement, finalized Nov. 28, paid $2.5 million to the Stevens family.

Scientists questioned

Before the settlement, Schuler questioned under oath several scientists whom the government had put on a list of witnesses for the civil trial. In their depositions, William Russell Byrne and Gerard Andrews, Ivins’ supervisors before and after the anthrax mailings, said they were virtually certain of his innocence.

Byrne said Ivins didn’t have the technical skill to make the extremely fine powder and both said the Fort Detrick lab’s equipment could not have dried the anthrax so it could be turned into powder without contaminating parts of the facility.

Prosecutors and FBI officials disputed the contentions of the two scientists, saying in interviews that they were biased because they supervised Ivins and could have missed signs of his guilt.

Vincent Lisi, assistant special agent in charge of the FBI’s Washington, D.C., Field Office, said Ivins, one of the nation’s most respected anthrax experts, “absolutely had the ability” to make the deadly spores and that experiments by FBI scientists showed there would have been no contamination.

Byrne and Andrews, in interviews, said they believe Ivins was not the killer.

“It is deeply insulting and slanderous to suggest that we were just kind of covering our butts,” Byrne said.

Four days after their disputed filings, Justice Department civil lawyers tried to file a “notice of errata,” and soon made a number of corrections and clarifications.

In September, the civil lawyers filed a sworn FBI declaration with nearly 60 points reaffirming Ivins’ guilt.