Evidence presented by several witnesses appearing before the Deputy State Coroner during the inquest into the suspected death of William Tyrrell have been heard in secret.
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In week two of the second round of hearings, the Deputy State Coroner Harriet Grahame moved to close the court for part of August 12 and 13.
Ms Grahame ruled it was in the interest of justice for some witnesses to give evidence behind closed doors.
A handful of the 54 people on a draft witnesses list have been assigned pseudonyms and granted permission to give evidence before just the coroner, lawyers and court staff.
The inquest into William's disappearance is being held five years after the three-year-old vanished while playing at his foster grandmother's home in Kendall.
Ms Grahame said she faced a difficult balancing exercise after media company Nine argued the court should remain open or, alternatively, evidence should be released in redacted transcripts.
Closing the court is a difficult step but it is sometimes necessary.
- Deupty State Coroner Harriet Grahame
Public scrutiny of the court and its processes was an important factor in delivering justice, Ms Grahame said, but publication had the potential to frustrate its operation.
"It may seem unusual (to close the court) ... but it is a regular process," Ms Grahame said.
"Not on a daily basis but it happens from time to time. Closing the court is a difficult step but it is sometimes necessary."
The Nine Network and Nine newspapers were supported in their application by a lawyer representing a previous person of interest in the case and William's biological father.
Peter O'Brien labelled the secret hearings "perplexing and unreasonable", adding he'd been prevented access to the court orders explaining who and why some witnesses would be heard behind closed doors.
"This should be as open as possible," the lawyer said.
Read more: William taken by a "sneaky, complex person"
Counsel assisting the coroner Gerald Craddock argued while it was frustrating for lawyers, the court needed to be closed in some circumstances.
"If it were possible to broaden the scope of those who have access to certain orders ... then we would do so," he said.
"It's wrong to say people haven't been considered."
The lawyer representing the NSW Police commissioner also opposed Nine's application.
Ms Grahame said the issue was not about freedom of speech or the press but the proper operation of justice.
A further 45 witnesses will be called in the next three weeks, including persons of interest who will appear before the Coroner when the inquest travels to Taree Courthouse from August 19.
So far, witnesses have included William's biological and foster families and emergency services personnel on the ground the day the toddler disappeared.
Mr Craddock said last week the absence of eyewitnesses and forensic evidence makes the investigation into William's suspected abduction among the hardest cases in the world to solve.
He reinforced that people called to give evidence will simply help put the pieces of the puzzle together and are not on trial.
All of the evidence collected by Strike Force Rosann is being presented before the Coroner who will determine if the three-year-old was abducted by someone. There is evidence yet to conclude that William is dead.
Newly appointed officer-in-charge of the investigation Detective Chief Inspector David Laidlaw - stepping into the role after the resignation of Detective Chief Inspector Gary Jubelin earlier this year over allegations of misconduct - is expected to give evidence.
