ALEXANDRIA, Va. — Dealing a blow to the government, a federal judge yesterday rejected an unprecedented prosecution proposal that would have kept secret large portions of a trial against two pro-Israel lobbyists.

Judge Thomas Ellis III ruled that the proposal, which would give jurors and court participants access to classified material that the public would be unable to see or hear, would unfairly “hobble” the defense, infringing on the constitutional and statutory rights of the lobbyists, Steven Rosen and Keith Weissman, to receive a public trial.

“I think the proposed procedure shackles the defense in a way that cannot pass muster” under the Classified Information Procedures Act, Judge Ellis said in court here yesterday, referring to the federal law that governs how classified material is presented at trial.

The government is charging Messrs. Rosen and Weissman with conspiring to obtain closely held national security information and pass it to American reporters and foreign diplomats while they worked as lobbyists for the American Israel Public Affairs Committee.

Under the prosecution proposal, known as the “silent witness” procedure, jurors and court participants would have listened to classified evidence through headphones and viewed secret documents on small screens that members of the public, including the press, would be barred from hearing or seeing.

The judge described the proposal as “novel” and even called it “fairly imaginative and creative,” but ultimately he ruled that it went too far. “Its use would appear to exclude the public from substantial and critical aspects of the trial,” he said. He listed a host of concerns about the proposal, including the use of codes that would be confusing to the jury and the possibility that jurors would have to be sworn to secrecy after the trial.

The decision was a significant setback for the government, which now must decide whether to declassify secret documents and recordings at the center of the case or come up with another way to present substitutions or summaries to the jury and the public. “We respectfully disagree with the court’s analysis of this proposal,” a prosecution attorney, Thomas Reilly, told the judge yesterday in asking for more time to confer with the Justice Department and the intelligence community.

Judge Ellis left open the possibility that the “silent witness” procedure could be used for isolated pieces of evidence, but he rejected its use “across the board.” He will rule individually on dozens of pieces of classified material, a process that he acknowledged could delay the start of the trial, now set for June 4.

The ruling was a victory not only for the defense but also for two groups — a consortium of news organizations and the Coalition for Jewish Concerns — that had sought to intervene in opposition to the “silent witness” procedure. The press group, the Reporters Committee for Freedom of the Press, criticized the proposal on First Amendment grounds, while the Coalition for Jewish Concerns, known as Amcha, argued that the secrecy could foment anti-Semitism by “perpetuating the myth of an overly powerful ‘Jewish lobby’ composed of people loyal to Israel first and the United States second.”

The judge rejected both groups’ attempts to intervene in the case. Nonetheless, they each embraced his decision. “Judge Ellis got it exactly right,” an attorney for Amcha, Steven Lieberman, said. “His ruling fully satisfies the concerns that we expressed.”