The musician made the announcement by sharing a heartfelt tribute on social media.
"Today I lost my father, Hugh Warner. He taught me how to be a man, a fighter and a survivor. He taught me how to shoot a gun. How to drive. How to lead.
"He will always be the best dad in the world. Somehow and somewhere, I know he is with my mom now. I will keep my promise and never let you down. I miss and love you dad," Manson, whose real name is Brian Warner, wrote in the caption, alongside a childhood photo of him with his dad.
The 48-year-old singer's mother, Barbara Warner, died in 2014 at age 68.
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