By Greg Gordon, McClatchy Newspapers, Mike Wiser, FRONTLINE, and Stephen Engelberg, ProPublica

WASHINGTON -- A senior Republican senator has asked the Justice Department to explain why its civil lawyers filed court papers questioning prosecutors’ conclusions that an Army researcher mailed the anthrax-laced letters that killed five people in 2001.

In a letter this week to Attorney General Eric Holder and FBI Director Robert Mueller, Sen. Charles Grassley of Iowa said the department’s decision to quickly retract the contradictory filings “has produced a new set of questions regarding this unsolved crime.”

Grassley, who's among several members of Congress who've been outspoken skeptics about the FBI’s conclusion, homed in on a development first reported collaboratively in July by PBS' "Frontline," McClatchy and the investigative newsroom ProPublica.

The Justice Department’s civil lawyers said July 15 in a major court filing in the case that Bruce Ivins, a now-deceased Army anthrax researcher whom the FBI has tagged as the killer, lacked access in his lab to the “specialized equipment” needed to dry wet anthrax spores into airborne powder that could be easily inhaled.

After hearing from the FBI and the department’s Criminal Division, the civil attorneys persuaded a federal judge in West Palm Beach, Fla., to permit 10 revisions to their position so it conformed with the FBI’s determination that Ivins did have equipment available to do the job.

Grassley, the ranking Republican on the Senate Judiciary Committee and a longtime FBI critic, said he wanted a briefing to “determine why it appears, at the least, that the right hand and left hand of the (Justice Department) do not know what the other is doing.”

Justice Department spokesman Dean Boyd declined to comment on the letter but said the department and the FBI "stand behind their findings that Dr. Ivins had the necessary equipment" to prepare the powder needed for the attacks and are confident they “would have proven his guilt beyond a reasonable doubt at a criminal trial."

The brouhaha developed as department lawyers sought to persuade a federal judge to dismiss an eight-year-old suit by the family of Bob Stevens, a photo editor for American Media Inc., in Boca Raton, Fla., who was the first person who died from the attacks.

The suit accuses the government of negligence, charging that it failed to adequately secure stocks of anthrax, one of the deadliest biological weapons, at the U.S. Army Medical Research Institute of Infectious Diseases at Fort Detrick in Frederick, Md.

The anthrax attacks killed five people in New York, Connecticut, Washington, D.C., and Florida, sickened 17 others and forced an estimated 30,000 people to take extended antibiotics therapy as a precaution. The $100 million, eight-year hunt for the perpetrator has been described as the most complex investigation in the FBI's history.

In his letter, sent Wednesday, Grassley said the Justice Department’s initial filing in the court case “seemingly eliminated” the government’s circumstantial case against Ivins, who committed suicide in 2008 after learning that prosecutors planned to seek his indictment on five counts of capital murder.

Grassley said he found the department’s contradictory filings “particularly troubling” because a National Academy of Sciences panel in February called into question the FBI’s assertion that genetic sequencing had definitively traced the source of the anthrax powder to a flask in Ivins’ lab. He noted that two USAMRIID scientists, in sworn depositions in the suit, disputed the FBI’s conclusion that Ivins could have made the powder in his laboratory.

Grassley also asked for an update on a prolonged investigation into news leaks that publicly identified another former USAMRIID microbiologist as a subject of the FBI investigation. That microbiologist, Stephen Hatfill, ultimately filed a privacy infringement suit against the government and obtained a $5.8 million court settlement.

One of the anthrax-filled letters was addressed to Democratic Sen. Patrick Leahy of Vermont, the chairman of the Senate Judiciary Committee, who also has expressed skepticism about the FBI’s finding that Ivins was the perpetrator.

This story was co-published with PBS "Frontline" and McClatchy.