The administration official said that Cartwright is suspected of revealing information about a highly classified effort to use a computer virus later dubbed Stuxnet to sabotage equipment in Iranian nuclear enrichment plants.
Stuxnet was part of a broader cyber campaign called Olympic Games that was disclosed by the New York Times last year as one of the first major efforts by the United States to use computer code as a destructive weapon against a key adversary.
Cartwright, who helped launch that campaign under President Bush and pushed for its escalation under Obama, was recently informed that he was a “target” of a wide-ranging Justice Department probe into the leak, according to the senior official, who spoke on the condition of anonymity because the investigation is ongoing.
Justice Department officials declined to comment on the case, as did Marcia Murphy, a spokeswoman for the U.S. attorney’s office in Maryland, which is in charge of the investigation.
Neither Cartwright nor his attorney, former White House counsel Greg Craig, responded to requests for comment.
The revelation, which was first reported by NBC News, means that an administration that has already launched more leaks prosecutions than all of its predecessors combined is now focused on one of its own. Since Obama took office, the Justice Department has prosecuted or charged eight people for alleged violations of the Espionage Act.
Cartwright was a regular participant in meetings of top national security officials at the White House and was thought to have significant influence with Obama before being passed over as a possible candidate to become chairman of the Joint Chiefs of Staff.
A target is a suspect in a criminal case who has not yet been indicted but is expected to be. Federal prosecutors are not required to tell targets that they are under investigation but it is not uncommon for them to do so in cases when an indictment is likely.
The investigation into the Stuxnet leak was launched in June 2012 by Attorney General Eric H. Holder Jr. and gained momentum in recent months amid indications that prosecutors were putting pressure on a range of current and former senior officials suspected of involvement.
The leaks surrounding Stuxnet exposed details about what had been one of the most closely held secrets in the U.S. intelligence community, an ambitious effort by the National Security Agency in collaboration with the Israeli government to devise computer code that could cripple Iran’s alleged effort to pursue a nuclear bomb.
The malware was designed to infiltrate Iranian computer networks and cause the nation’s centrifuges to spin out of control, causing damage to critical equipment and sowing confusion among Iranian scientists.
The campaign is believed to have destroyed as many as 1,000 of Iran’s 6,000 centrifuges at the time. But the virus also escaped those closed systems and was subsequently discovered on the Internet, raising concern about the potential that government-sponsored viruses could cause widespread and unintentional harm.
Cartwright, who previously served as head of U.S. Strategic Command, was a principal architect of the campaign. His role, a former senior official said in an interview last year, “was describing the art of the possible, having a view or vision.”
Cartwright, 63, went on to be named to the Pentagon’s No. 2 military post, moving him to the center of policy issues ranging from Iran to the pursuit of al-Qaeda in Pakistan and Yemen.
As vice chairman, Cartwright was scorned by many fellow senior generals for opposing a plan in 2009 to dispatch tens of thousands more troops to Afghanistan, putting him at odds with former peers, including Gen. David H. Petraeus, but earning him favor with senior Obama national security aides.
Although Obama forged a quick rapport with Cartwright — White House officials referred to him as the president’s favorite general — the president chose not to promote him to chairman in 2011, in part because of concern that Cartwright had frayed his relationships with too many senior generals during the surge debate. Within the Pentagon, “he wasn’t seen as a team player,” said a senior military official who worked on the Joint Staff.
After retiring, Cartwright took a position at the Center for Strategic and International Studies and has spoken frequently on national security issues. He has emerged as a growing critic of the Obama administration's expanded use of drones to counter the al-Qaeda threat.
At at event in Chicago in March, Cartwright said that the United States was beginning to see “blowback” from that targeted killing campaign. “If you’re trying to kill your way to a solution, no matter how precise you are, you’re going to upset people even if they’re not targeted.”
Peter Finn, Rajiv Chandrasekaran and Ellen Nakashima contributed to this report.