Edinburgh-born Manson, who was back in Scotland to collect an outstanding achievement honour at the Scottish Music Awards, said changing attitudes towards female performers had brought criticism on Cyrus.
The 47-year-old said “nobody batted an eyelid” in the mid-1990s when she wore see-through dresses and grabbed her crotch on stage.
Manson spoke out on the issue just weeks after fellow Scot Annie Lennox said she had been left “disturbed and dismayed” by a growing music industry trend for “highly-styled pornography with musical accompaniment.”
The former Eurythmics star, 58, intervened following a bitter spat between Cyrus, whose video for the song Wrecking Ball features her swinging naked on a demolition ball, and Irish singer Sinead O’Connor. Cyrus had earlier sparked worldwide controversy with her on-stage performance at the MTV Awards in Los Angeles.
Lennox also said she was depressed at how many performers were prepared to behave like “pimp and prostitute at the same time.”
However Manson said: “I disagree in some ways with how Miley has been castigated. I think it’s a very complex issue.
“But put it this way - when I was starting out with Garbage in the 1990s, I wore see-through dresses, and I used to grab my crotch and my boobs.
“Nobody batted an eyelid at the time. Nobody castigated me. But she has been treated like the antichrist.
“Artists make their own decisions and know there may be repercussions. It is up to them.”