Held three years before the outbreak of the Second World War, the 1936 games are widely remembered as a propaganda coup for Adolf Hitler's Nazi regime.
In March this year, Berlin's state minister of the interior Andreas Geisel faced heavy criticism after he appeared to suggest Berlin should bid for the 2036 Olympics in an interview with Tagesspiegel newspaper.
However, the 69-year-old Seehofer, whose ministry also holds the sports portfolio, said Germany could not be seen to celebrate the centenary of the Nazi-era Berlin Olympics.
"It would be unthinkable. If we did that, we would bring on an unspeakable international discussion and harm the Olympic idea," he told Frankfurt-based newspaper Frankfurter Allgemeine Zeitung (FAZ) in an interview published on Monday.
"How would people see it across the world? Germany celebrating the 100-year anniversary of the Nazi Olympics? That cannot happen."
Aside from concerns over associations with the Nazi regime, there is scant public support for hosting the Olympics in Germany.
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Public referendums, in 2015 and 2013, rejected proposed Olympic bids to host the summer games in Hamburg and a winter edition in Munich respectively.
Seehofer said that he was generally in favour of a German Olympic bid, but voiced concern that the International Olympic Committee (IOC) had become too focused on commercial success.
"In the eyes of the public, the IOC has wandered too far from its original idea and into commercialism," he told the FAZ.
He called on the IOC to "de-commercialise" and said he had "a lot of sympathy" for the German Athletes' Commission, which last year demanded that the IOC share a quarter of its profits with Olympic participants.
By Kit Holden
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