The Seoul District Prosecutors' Office said the pair are accused of acquiring a four-page classified document about South Korea's submarine acquisition project from a navy captain.
The two are former naval officers working for German shipbuilder Howaldtswerke-Deutsche Werft, it said. They were not detained.
The navy captain is under investigation by military prosecutors, the office said.
The Germany company has provided technology to help South Korea build nine 209-Class and two 1,800-ton 214-class submarines.
South Korea plans to build seven more 214-class submarines by 2018. It has also launched a 2.7 billion dollar project to develop its own technology to build 3,000-ton submarines in 2018.
South Korea, which deploys a 680,000-strong military against a potential threat from communist North Korea, is sensitive about defence secrets.
In March 2006 an executive of French defence company Thales was charged with obtaining classified documents concerning radar equipment for the navy. He was later acquitted.