The 49-year-old actress, who is a recovering drug addict, made the statement in her new autobiography High On Arrival.
She claims that she slept with her father the night before her wedding when she was 19 years old.
"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," she writes.
According to Entertainment Tonight, the star also discussed the allegations during an appearance on The Oprah Winfrey Show today, saying that the relationship continued for ten years.
"It didn't happen every day, didn't happen every week, but it did happen many times. It became a consensual relationship over time," she is quoted as saying.
Phillips reportedly added that the affair was influenced by the pair's heavy reliance on drugs at that time.
John Phillips died of a heart attack in 2001 aged 65.