Bavarian chief prosecutor Christian Haertl told the BR24 radio that the man died in September, bringing an investigation into his alleged role in prosecuting camp inmates to a premature close.
The suspect is believed to have arrived at the camp in January 1945, months before it was liberated by the Allies.
The investigation was opened in April to determine how long the suspect was employed at the camp. He was purportedly the last known guard from an elite SS unit posted to Flossenburg during World War II.