Heinrich Mueller, who was the head of the Nazi Gestapo secret police, was buried in a Jewish cemetery, reported German newspaper Bild.
The discovery was made by Johannes Tuchel of the German Resistance Memorial Center after finding documents that were hidden away in city archives.
"(Mueller's) corpse was buried in a mass grave in the Jewish cemetery in Berlin Mitte," he said.
Mueller was long rumored to have survived World War II. Bild quoted a German BND foreign intelligence file stating that Mueller was in Carlsbad in the former Czechoslovakia in summer 1949.
But Tuchel told the newspaper that the secret services were wrong.
"Mueller's body was already found in August 1945 in a provisional grave near the former Reich's aviation ministry by a burial commando," he told Bild.
His body was dressed in a general's uniform, Tuchel said. "In the inner left breast pocket was, among other things, his service certificate with a photo," he went on.
Bild also printed a document it said was from the registrar's office in Berlin-Mitte showing Mueller was buried in the district's Jewish cemetery.
The leader of Germany's Jewish community, Dieter Graumann, reacted angrily to the revelation.
"That one of the most brutal Nazi sadists is buried in a Jewish cemetery is a distasteful monstrosity. The memory of the victims is being treated here with contempt," he told Bild.
Mueller attended the Wannsee Conference at a villa on the outskirts of Berlin in January 1942 at which senior Nazis plotted the "Final Solution", a plan to exterminate all Jews in Nazi-occupied Europe.
Mueller was last seen in May 1945 in Adolf Hitler's bunker, and investigations regarding his fate continued for decades after World War 2.
Gravedigger Walter Luders told police in 1963 that he had buried Mueller personally in the Jewish cemetery, and that he had seen Mueller's face. Luders' statement now turns out to have been true.