Radiohead's Thom Yorke said he was told of the performance by text message and thought it "hilarious".
But when he was informed he could not see the song, for which his band owns the copyright, he was baffled.
"Really? He's blocked it?" Yorke was reported to have said. "Surely we should block it. Hang on a moment ... well tell him to unblock it, it's our song."
YouTube bans the posting of copyright material and removes the video if it receives a complaint from the owner of the copyright.
Last year Prince threatened to sue thousands of his fans for breach of copyright, forcing three fansites to remove all images, lyrics, and album covers. The artist, who once temporarily changed his name to a symbol, is believed to take a close interest in the use of his image, monitoring websites using his music.
Radiohead released their last album, In Rainbows, as a digital download, allowing fans to pay as much as they thought it worth. The Prince video, filmed by fans at the Coachella Valley festival in Indio, California on April 26, was last night reposted on YouTube.
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