The singer, who is currently in the process of divorcing Miley's mother Tish, said that Miley's "handlers" are to blame for her change in attitude.
He told GQ: "Every time the train went off the track, her people, or as they say in today's news, her handlers, every time they'd put the blame on me. I took it because I'm her daddy. Okay, nail me to the cross.
"I'm scared for her. She's got a lot of people around her putting her in a great deal of danger. I want to get her sheltered from the storm."
Billy Ray also admitted that he didn't attend Miley's 18th birthday party in case he was blamed for the fact that it was held at a bar, when she is three years under the legal age for drinking alcohol in the US. She was also recently videoed smoking a legal high through a bong device.
He explained: "You know why I didn't go? Because they were having it in a bar. It was wrong. It was for 21 years old and up. All them people, they all wanted me to fly out so that then when all the bad press came they could say, 'Daddy endorsed this stuff.' I started realising I'm being used.
"After the incident with the legal high, her handlers told me it was none of my business. I should have said, 'Enough is enough - it's getting dangerous and somebody's going to get hurt'. Honestly, I didn't know the ball was out of bounds until it was way up in the stands somewhere."
Miley became famous after appearing on Disney TV show Hannah Montana, with Billy Ray playing her father, but he has admitted that he regrets doing the show.
He added: "The damn show destroyed my family. I hate to say it, but I'd take it back in a second."