Judge Clarkson's criticism, in a ruling released yesterday, was made after the mother and father both applied for custody of the four children aged 13, 9, 8 and 3.
She determined that neither parent was able to care for the children, and ordered that the youngsters be removed from the home.
But the judge's more-severe comments were reserved for Child, Youth and Family (CYF).
"Quite apart from the disappointing lack of protection of these four children, I am left wondering if this is indicative of CYF's practice."
She said despite police, family members and teachers repeatedly bringing the case to the attention of the government agency, the children were left with their parents.
"Because I consider that the deficiencies in CYF's performance in this case have been so serious, I propose to refer this decision to the Commissioner for Children for further investigation."
Jane Drumm described the case as a "systems failure", the like of which she had never seen before.
At times, the children were left in the care of their father, who had a conviction for repeatedly raping his 14-year-old niece.
They were also left in the care of their mother, who on one occasion left two of them in a carpark in South Auckland. A member of the public complained. Police responded two hours later and found the children with chicken, bread and juice.
"On returning to her car, she [the mother] apparently showed little concern," Judge Clarkson said.
The woman told police she had been in the Manukau District Court to see her husband's court case. At the time, he had active charges of rape, threatening to kill and assault.
Judge Clarkson said there were 20 notifications to CYF over nine years.
In October 2004, a family member made an anonymous complaint after one of the children - then aged 5 - was found with a cut to her head.
CYF found that the mother had abused the child but because the youngster was still in the care of the mother, "she was unable to be interviewed", Judge Clarkson's ruling said.
A "whanau agreement" was entered into but there were no records to show the result.
"This response by the Ministry (of Social Development, CYF's overseer) to what they recognised as established physical abuse on this child can only be described as reckless."
On one occasion, three of the children were inside their father's car when the mother smashed the windscreen and passenger window with a steel pipe.
CYF referred the matter to a community-based programme before closing the case.
On another occasion, the father shattered windows, punched five holes in the wall, broke two mirrors and smashed a coffee table to pieces.
After a discussion between CYF and police, "it was deemed that no action was required", Judge Clarkson's ruling said.
Under questioning in court, a CYF social worker supervisor conceded: "I probably would have done things a bit differently with some of the history we've had over the years."
Ms Drumm said it took a lot for people to phone CYF and she hoped they continued to. "This is as bad as it gets." She said it was appalling that CYF could allow the children to be in the care of a man who had a conviction for raping a minor.
"All these children have been witnesses to terrible abuse for years and years - their whole life - and it is really difficult to come back from that. They've had no childhood, no love and no care," she said.
A spokeswoman for Children's Commissioner Dr Russell Wills said the office expected to receive the judge's finding next week.
She said a team from the office would look into the issues and report back to the judge, but it was unlikely the findings would be made public.
Neglect and inaction
October, 2003: Father assaults mother and their 4-year-old, who is left with a blood nose. CYF removes the children but returns them to the parents the following year.
March 2004: Mother tells hospital staff of ongoing violence. CYF closes the file "due to a delay in the information being provided".
September 2006: Seven-year-old daughter tells her teacher that she and her younger sister have been hit. There are also unexplained absences from school.
