Correction: An earlier version of this article failed to mention that a joint report by McClatchy newspapers, PBS’s “Frontline” and ProPublica first disclosed the court documents in the Florida anthrax death case. This version includes that information.

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

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

Now, in the latest twist, the government has argued against itself.

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

The spectacle of one arm of the Justice Department publicly questioning another could 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,’’ 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. His survivors accused the government of negligence for experimenting with anthrax at Fort Detrick; the case lingered in court until the Justice Department settled it in November.

The court documents in the case were first disclosed in a joint report by McClatchy newspapers, PBS’s “Frontline” and ProPublica.

The case, Stevens v. United States, offers a rare glimpse inside a typically unified and notoriously tight-lipped agency that collided with itself in a particularly controversial investigation. While the guilt of Ivins is likely to be a subject of public speculation and intrigue for years to come, the government’s inconsistency in the Stevens matter is sure to add another layer to that debate.

Justice Department prosecutors and FBI officials said they stand firmly 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 that their conclusions had apparently been challenged — and by their colleagues, no less — 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 that 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’s guilt, someone higher up in the department should have seen this collision coming down the tracks,’’ Rothstein said.

Confusion raised doubts

Critics said that 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’s colleagues and some members of Congress — has long questioned his guilt.

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

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

Department officials acknowledged that the civil filings appeared contradictory but attributed that 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 in the U.S. Attorney’s Office in the District who would have led the prosecution of Ivins. “People are entitled to their own views, but if you take a rational approach and look at the evidence, you come to the conclusion that it’s overwhelming.”

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’s flask of anthrax spores to the attacks.

Conflicts with criminal side

That conflicted with the department’s criminal side, which had closely linked Ivins, his lab and the deadly anthrax. The FBI had strongly suggested Ivins prepared the killer spores in the lab, pointing to the anthrax he maintained there, highly 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 to describe internal matters. “If you file something in court that you don’t word perfectly and you have to go back and refile it, you should get yelled at for that.”

Richard Schuler, an attorney for the Stevens family, said “there’s no question” that the government’s decision to avoid a trial in the civil case was related to the conflicting evidence. “They would have been in the position of potentially going against their own investigative agency, the FBI,” he said.

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

Federal officials denied any relationship between their filings and the settlement and characterized it as a victory, since the family initially sought $50 million and the government did not admit liability.

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 P. Andrews, Ivins’s 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. Though Byrne and Andrews were listed as government witnesses in the civil case, officials said they would never have been certified by a judge as experts under the stricter rules in the criminal system, which does not allow speculation.

Vincent B. Lisi, assistant special agent in charge of the FBI’s Washington Field Office, said in an interview that 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 continued to believe Ivins was not the killer. “It is deeply insulting and slanderous to suggest that we were just kind of covering our butts,” said Byrne.

When Justice Department lawyers filed their July motions in the civil case, they wrote that the deadly powder would have required a certain amount of liquid anthrax — and the liquid content of anthrax created by Ivins and stored in a flask labeled RMR-1029 wasn’t nearly enough.

And though the department’s criminal side had said all other suspects were ruled out, the civil lawyers said portions of RMR-1029 had been sent before the attacks to Battelle, the Ohio-based lab. They raised a possible scenario in which the attack anthrax could have come from the anthrax at that lab or other labs to which Battelle may have transferred the spores.

Katy Delaney, a spokeswoman for Battelle, did not respond directly to the government filings, but said “the Stevens case against Battelle was dismissed and the [criminal] investigation of Battelle has been closed.”

Justice Department and FBI officials reiterated in interviews that they exhaustively investigated the 42 people at Battelle with access to the anthrax and ruled them out as suspects.

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’s guilt.

Stephen A. Saltzburg, a law professor at George Washington University and former Justice Department official, said the department was right to pull the plug on the civil case but should have done so earlier.

“It would have been treacherous for them to litigate this, to answer all the questions their own pleadings raised,’’ he said. “In many ways, it was the government arguing against itself.’’