Officers handed the boy, who is understood to be Indigenous, the order issued by the Perth Children's Court on Friday.
Commissioner Col Blanch said violence restraining orders can't be issued to anyone under the age of 10 and the court shouldn't have issued the order to police.
He said the court failed to put the child's date of birth on the VRO and a young police officer had issued it to the boy, who was with his family.
"I'm not going to criticise the young police officers," he told 6PR radio on Tuesday.
Mr Blanch said it was a "system issue" that he would have to fix with the courts.
"We've gone out to the family, we've apologised to Mum (and) we've spoken to the boy," he said.
"We don't want to do these things ... they're a battling family and they were a good family talking to them this morning and we've just got to fix it up."
Aboriginal Affairs Minister Tony Buti said it was very distressing but officers had been acting on a court order.
"When they got back to the police station, I believe they then realised the situation," he said.
"So they're acting according to what they thought was the appropriate measures but of course, it's something that's been very distressing."
A court spokeswoman said the order was cancelled on Monday after police advised the boy was aged seven.
"The court has checked the hearing of the original application and the representation made to the court was that the children the subject of the applications were in high school," she said.
"The court also made an order that the applicant for the order be personally served with the cancellation notice."
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