However, CYF officials say they are comfortable with the arrangement and the stepfather is not staying with the boy while the investigation is carried out.
The boy's parents are separated and share custody of the boy.
The family spokesman said when the child initially complained about a sore stomach it was thought it was related to food.
After persistent complaints, the abuse allegations emerged.
After police staff had interviewed the child, last Monday at CYF's Walton St office, CYF had decided to release the boy back into his mother's care.
Both were living with a family member, without the stepfather, while investigations continued.
"CYF said there was a parental order which was working and the mum had promised he [the stepfather] wouldn't visit them; basically that there were no safety issues," the family spokesman said.
Child, Youth and Family regional director Marion Heeney said her staff had worked closely with police and Whangarei Hospital in investigating the case.
She said the boy was now living with his mother and grandparents at the latters' home while the investigation was carried out.
"He is not to have contact with his stepfather.
"As part of this arrangement the young boy will continue to stay with his father on weekends."
Ms Heeney said CYF would continue to work with the boy's family to ensure his ongoing safety and well-being.
She said consideration needed to be given to the individual circumstances of each case before decisions could be made around what support or action was needed.
"As police investigations can often be complex and lengthy, Child, Youth and Family may have to act before they are complete to ensure a child's safety."
Those decisions were made on a case-by-case basis, Ms Heeney said.
