Nearly 700 people were in the investigators' sights last year and in September a A$1 million ($1.1m) reward for information on William's disappearance was announced.
When William disappeared from the house in Kendall, he was under the control of the Department of Family and Community Services (Facs), being cared for by foster parents in what is referred to as out-of-home care.
Facs had guarded this secret until now, the programme said, but it provides another missing piece in the puzzle that has captured Australia.
There's no suggestion that either William's biological or foster families were involved in his disappearance or have any knowledge of his whereabouts.
Nor is there suggestion of fault on their parts.
William's biological father had struggled continually with drug and alcohol problems and life behind bars, A Current Affair said.
Meanwhile, William's loving foster parents, who have not shared their identities, still hope he is alive.
"If he is alive, if somebody has him, I want him to be feeling loved, I want him to be safe," William's foster mother said.
In the Court of Appeal documents, the judge found that the fact that William was the responsibility of the NSW Minister for Family and Community Services, and in the care of departmentally approved carers, was a matter of "legitimate public interest".
Supreme Court of NSW judge Justice Brereton is also quoted as noting "the tragic probability that [William] is no longer alive".
