The Nazi deputy's remains were exhumed, burned and scattered at sea after his grave became a shrine.
Neo-Nazis liked to gather at the site to pay homage to Hess.
The Lutheran church refused to extend a lease on the plot.
The remains of Adolf Hitler's one-time deputy Rudolf Hess have been exhumed in Germany and his grave destroyed after it became a shrine for neo-Nazis, authorities said Thursday.
The monument was razed on Wednesday "in an operation not open to the public," said Roland Schoeffel, deputy mayor of the village of Wunsiedel, southern Germany.
The remains of Hess were removed at dawn and were due to be cremated and scattered at sea, the Sueddeutsche Zeitung reported.
Hess was buried according to his wishes in Wunsiedel churchyard in Bavaria after his 1987 suicide in a Berlin prison aged 93. His gravestone read "Ich hab's gewagt" ("I dared.")
But because of neo-Nazis paying homage, including performing Hitler salutes in the churchyard, the Lutheran church's council refused a request by Hess's descendants to extend a lease on the plot, council member Peter Seisser said.
After letters were written to the family explaining how the grave was becoming a shrine, Hess's granddaughter held talks with the council and agreed for it to be removed.
"She said she wanted nothing more to do with it," said Seisser. "We were all very relieved."
Hess parachuted into Scotland in an apparent peace mission in 1941 without Hitler's approval. He was kept prisoner for the remainder of World War II before being sentenced to life imprisonment at the Nuremberg trials in 1946.
From 1966 onwards, he was held as the sole prisoner at Spandau Prison in West Berlin until he was found hanged in August 1987.