"The minister cancelled his visit. The ceremony has been postponed indefinitely," said Federica Scotellaro, a spokeswoman for Ca' Foscari University.
"We are not denying him the award," she said.
Medinsky had been due to receive the award on Monday, but a petition signed by 100 lecturers complained about comments made by the minister about Russian culture.
Alessandro Casellato, a member of the university's Academic Senate, was quoted by the local Venice daily Il Gazzettino as saying that the minister was "controversial because of his political positions".
Medinsky last month portrayed contemporary European culture as depraved, saying: "Perhaps Russia will be the last keeper of European culture, Christian values and truly European civilization."
Russia "is forced to culturally protect itself," he said.
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The Kremlin is preparing a new culture policy for Russia focusing on its distinctive civilization and traditional values, which observers say has political ends amid Moscow's standoff with the West over Ukraine.