In this April 21, 2011, file photo, Gen. James Cartwright, then vice chairman of the Joint Chiefs of Staff, talks to reporters alonside then-Defense Secretary Robert Gates. (Alex Brandon/AP)

A sensitive leak investigation of a former vice chairman of the Joint Chiefs of Staff has stalled amid concerns that a prosecution in federal court could force the government to confirm a joint U.S.-Israeli covert operation targeting Iran, according to current and former U.S. officials.

Federal investigators suspect that retired Marine Gen. James E. “Hoss” Cartwright leaked to a New York Times reporter details about a highly classified operation to hobble Iran’s nuclear enrichment capability through cyber-sabotage — an effort not acknowledged by Israel or the United States.

Prosecutors will have to overcome significant national security and diplomatic concerns if they want to move forward, including pitting the Obama administration against Israel if that ally were opposed to any information about the cyber-operation being revealed in court.

The United States could move forward with the case against Israel’s ­wishes, but such a move might further harm relations between two countries, which are already frayed because of a disagreement over how best to prevent Iran from obtaining nuclear weapons.

Administration officials also fear that any revelations could complicate the current negotiations with Iran over its nuclear program.

“There are always legitimate national security reasons for not proceeding in one of these ­cases,” said John L. Martin, who handled many sensitive espionage investigations as a former Justice Department prosecutor.

The case captures the tension between national security concerns and the desire of prosecutors to hold high-ranking officials to account for leaking classified secrets. The Obama administration has been the most aggressive in U.S. history in pursuing those suspected of leaking classified information.

The Justice Department has offered no clues to whether it intends to proceed with a case against Cartwright, who helped design the cyber-campaign against Iran under President George W. Bush and was involved in its escalation under President Obama.

Spokesmen for the Justice Department, the White House and the FBI declined to comment for this article.

Gregory B. Craig, Cartwright’s attorney and a former White House counsel in the Obama administration, said he has had no contact with prosecutors for more than a year.

“General Cartwright has done nothing wrong,” Craig said. “He has devoted his entire life to defending the United States. He would never do anything to weaken our national defense or undermine our national security. Hoss Cartwright is a national treasure, a genuine hero and a great patriot.”

In discussions with the office of the White House counsel, then led by Kathryn Ruemmler, prosecutors sought to determine whether the White House would be willing to declassify material important to the case. Ruemmler was unwilling to provide the documentation, citing security concerns, including those relating to sources­ and methods, said a person familiar with the matter.

Ruemmler, who left the post in June, declined to comment.

“There’s a fundamental tension in cases­­ like this between the needs of a criminal prosecution and the needs of national security,” said Jason Weinstein, a former deputy assistant attorney general in charge of the Justice Department’s Criminal Division, who was not briefed on the investigation. “Where that comes to a head is when prosecutors want to use evidence in a courtroom that is highly classified and very sensitive.”

It is often the case that the needs of a particular criminal prosecution yield to national security interests. “At the end of the day,” Weinstein said, “if you can’t use the evidence you need in court, you can’t bring the case.”

Details of the joint program, including its code name, Olympic Games, were revealed by Times reporter David E. Sanger in a book and article in June 2012. The sabotage of Iranian nuclear centrifuges by the computer worm dubbed Stuxnet had emerged two years earlier, and security experts speculated that it was the work of the United States and Israel.

Confirmation of the joint authorship set off a political controversy, with congressional Republicans charging that the White House had deliberately leaked information to enhance Obama’s national security credentials as he sought reelection.

Attorney General Eric H. Holder Jr. assigned Rod J. Rosenstein, the U.S. attorney for Maryland, to investigate the leak. His office declined to comment.

FBI investigators focused on Cartwright in the fall of 2012, officials said. They interviewed him at least twice, according to people who are familiar with the case and who spoke on the condition of anonymity because of the sensitivity of the investigation. During the first interview, Cartwright had to go to the hospital.

Part of the challenge of preparing a case like this is determining to what extent authorities who control the declassification of information, in this case the White House and the intelligence community, are willing to divulge information.

In the case of a CIA officer who was recently convicted of espionage, the government disclosed sensitive details during the leak trial about a separate operation to sabotage Iran’s nuclear program that occurred more than a decade ago. The CIA even allowed a Russian scientist who had defected and taken part in the highly classified operation to testify.

“The government’s got to make a choice: Is it more important to prosecute a national security leak or more important to preserve relationships with allies and shield sources­ and methods that protect the country?” said one individual familiar with the matter.

The case also poses opportunities for “graymail” — a situation in which defense attorneys exercise leverage that lawyers in ordinary criminal cases­ lack by forcing prosecutors to make tough judgment calls about divulging sensitive or classified information.

Craig might, for instance, push for broad discovery of information aimed at demonstrating that other officials could have been sources­ of the leak. Experts say he also could press to establish the factual basis for the information leaked, which could expose sensitive material.

Cartwright, who retired in 2011, had White House authorization to speak with reporters, according to people familiar with the matter. Craig might try to put the White House’s relationship with reporters and the use of authorized leaks on display, creating a potentially embarrassing distraction for the administration.

The case could remain open beyond the point at which national security and foreign policy concerns are an issue. Under the Espionage Act, one of the statutes that the government probably would use, prosecutors have 10 years from the date of the alleged crime to file charges.

Sari Horwitz contributed to this report.