Another Blackwater employee involved in the case, Jeremy P. Ridgeway, previously pleaded guilty to charges stemming from the shootings and was cooperating with prosecutors.

A Justice Department spokesman, Dean Boyd, said no decision had been made about whether to appeal the judge’s ruling.

“We’re still in the process of reviewing the opinion and considering our options,” Mr. Boyd said.

But Judge Urbina’s scathing and detailed review of the ways that crucial evidence and witnesses had been tainted by exposure to the defendants’ early statements  or to news media accounts based on them  appears likely to complicate any effort to ask an appeals court to overturn his opinion or to bring a new prosecution by a different legal team using any untainted evidence.

Daniel C. Richman, a former federal prosecutor who teaches criminal law at Columbia University, said that it was rare to have a judge issue a lengthy opinion at a pretrial stage. While cautioning that he had not read the opinion, he said that rulings like this one, consisting heavily of factual findings rather than merely legal interpretation, were “hard to challenge on appeal.”

The guards could not be prosecuted under Iraqi law because of an immunity agreement that had been signed by the Coalition Provisional Authority, the governing authority installed by the United States after the invasion of Iraq. But American prosecutors knew from the beginning that they were facing a difficult task in bringing the case. Complications included the applicability of federal statutes to the guards because they were working overseas at the time for the State Department, and the significant problem stemming from statements the guards gave shortly after the shootings.

The guards had been told by State Department investigators that they could be fired if they did not talk about the case, but that whatever they said would not be used against them in any criminal proceeding.

Nevertheless, Judge Urbina found that “in their zeal to bring charges,” investigators and prosecutors had extensively used those statements, disregarding “the warning of experienced, senior prosecutors” that “the course of action threatened the viability of prosecution.”