Judge Janice Cunningham called the situation "scary", but added: "I recognise that Mr Margraves had three daughters that he has had to watch go through the pain and the hurt. I can't imagine what it is like for a parent."
The distraught father was later brought before the judge in handcuffs, and apologised to everyone in the courtroom, saying he was "embarrassed".
"I'm not here to upstage my daughters, I'm here to help them heal," he said.
"I got to hear that, and I got to see Larry Nassar over here shaking his head 'no,' like it didn't happen," Mr Margraves said.
The judge accepted his apology, and confirmed he will not face contempt of court charges.
"There is no way that this court is going to issue any type of punishment, given the circumstances of this case," Judge Cunningham said.
"My heart does go out to you and your family for what has happened to you."