The five-year-old boy is currently being treated by specialists for problems with his behavior learning, language and motor skills, the Herald Sun reports.
The Federal Magistrates Court was told that if the boy were ever left in his grandfather's care, he would be subjected to various "treatments" that could result in harm.
The grandfather had subjected the mother to an "intrusive and abusive" upbringing, the court heard, including two years of "emotional release therapy" to supposedly help her through bullying at school.
One treatment involved "reliving her birth".
A court-appointed doctor said the grandfather had poor personal boundaries and an "idiosyncratic" belief system he had "imposed on the mother in the past, to the detriment of her mental health". The mother and grandparents only recently repaired their relationship.
But magistrate Robyn Sexton said she believed neither the mother nor grandmother were able to stand up to the grandfather and stop him "practicing his treatment".
He was banned from having the boy in his sole car and restrained from giving the boy any therapy or counselling.