Yair Ramati headed the ministry's missile-defense program, a position he held for four years.
The ministry announced Ramati's dismissal late Sunday. It gave no further details, but defense officials said he had kept sensitive information on his personal computer. The officials spoke on condition of anonymity because they were not authorized to talk to the media.
Yitzhak Ben Israel, the head of Israel's space agency and a friend of Ramati's, told Israeli Army Radio that any information breach was done "unknowingly."
But Ben Israel said that if the information was exposed, there was the possibility of "real damage."
Israel is considered a world leader in missile-defense technology. It is developing a multilayered system with defenses against everything from long-range guided missile attacks from Iran to crude rockets fired from Lebanon and the Gaza Strip.
Its rocket-defense system, Iron Dome, was considered a great success during last year's war against Gaza militants, when it intercepted hundreds of incoming rockets. Ramati just last week lauded the successful final testing of a U.S. And Israeli developed missile-defense system called "David's Sling." He has seen through other important defense projects during his tenure.