Retired Marine Gen. James Hoss Cartwright, who was Joint Chiefs vice chairman, allegedly leaked information about a U.S. virus attack on Iran's nuclear facilities, the sources said.
Cartwright, 63, is the latest individual targeted because of alleged leaks. The government has prosecuted or charged eight people under the Espionage Act.
The New York Times reported in 2012 that President Barack Obama ordered a cyberattack in 2010 using the Stuxnet virus, which temporarily disabled 1,000 centrifuges that the Iranians were using to enrich uranium.
The Times story included details of a covert Olympic Games operation, which Cartwright ran under President George Bush and Obama.
Details in the story included meetings in the White House Situation Room and the way the virus was introduced to an Iranian nuclear facility.
As soon as the story appeared, Congressional leaders demanded an investigation.
Two sources told NBC that prosecutors were able to identify Cartwright as a suspected leaker without resorting to a subpoena of reporters' phone records.
Cartwright declined to comment on the allegations, NBC News said.