The former child star claims she was just 19 when The Mamas & The Papas singer raped her on the eve of her wedding to Jeff Sessler in 1979.
She writes in her new memoir High on Arrival, "On the eve of my wedding, my father showed up, determined to stop it (the wedding). I had tons of pills, and Dad had tons of everything too. Eventually I passed out on Dad's bed.
"My father was not a man with boundaries. He was full of love, and he was sick with drugs. I woke up that night from a blackout to find myself having sex with my own father. Had this happened before? I didn't know. All I can say is it was the first time I was aware of it. For a moment I was in my body, in that horrible truth, and then I slid back into a blackout."
The incestuous relationship between John and Mackenzie, from his first marriage to socialite Susan Adams, later became consensual as the pair began using heroin together and touring in a band called The New Mamas and The Papas.
Wilson Phillips founder Chynna reveals she received a phone call confession in 1997 from her half sister, who revealed her affair with their father began while he was married to third wife, Genevieve Waite.
Standing by her sister, Chynna tells U.S. magazine Us Weekly, "They were both doing drugs together. After long nights of heroin use, she's claiming that she once woke up and that my father was on top of her having sex with her. Was he actually raping her? I don't know. Do I believe they had an incestuous relationship and that it went on for 10 years? Yes."
However, Chynna's actress mum Michelle Phillips, John's second wife and former member of The Mamas & The Papas, has rejected Mackenzie's claims as the musings of a desperate drug addict.
She adds, "You should take with a grain of salt anything that's said by a person who has had a needle stuck in their arm for 35 years. The whole story is disgusting."
John Phillips died of heart failure in 2001, aged 65.