Despite extensive investigations and a reward offer of $1 million, the boy has never been found

While Chief Inspector Jubelin has been taken off the investigation, a police spokesman confirmed that the coronial inquest into William's disappearance would go ahead later this month as planned.

Detective Chief Inspector Jubelin has not taken leave, but remains at work in the homicide squad on a range of other matters.

In September, the Herald revealed the State Coroner would investigate what happened to the little boy after four years of police investigation had failed to solve the presumed abduction.

On Friday Acting Assistant Commissioner Stuart Smith said an allegation of misconduct was referred to the Professional Standards Command earlier this year, but watered down any suggestion that it would impact the upcoming inquest.

"There are 26 other investigators that have all worked on the William tyrrell strike force diligently...the matter will proceed to inquest in the hands of the state's most senior homicide inspector David Laidlaw," he said.

He said the welfare of Chief Inspector Jubelin was "foremost," and the allegations against him would now "move through the system."

Chief Inspector Jubelin attended a directions hearing with William's foster parents in December ahead of the inquest.

At the time, he told reporters that police continued to probe the disappearance.

"It’s a matter before the coroner, but it is an active investigation," he said.

Police have sifted through more than 15,000 pieces of evidence and interviewed more than 600 persons of interest in the hopes of discovering what happened to William.

Last June, a four-week search in the bushland surrounding the house failed to yield any clues.

Chief Inspector Jubelin has worked on a number of other high-profile homicide cases, including the disappearance of three Indigenous children from Bowraville, the death of bikie associate Clint Stanley and the death of Matthew Leveson.

On Friday, the parents of Mr Leveson, whose body was found buried in the Royal National Park in 2017 after a decade-long search, expressed their shock at Chief Inspector Jubelin's removal from the Tyrrell investigation.

"It was more than a surprise. It was upsetting to think somebody would throw those accusations at him," Faye Leveson told the Herald.

"For Matty, he was nothing but professional, caring and compassionate. He puts his all into a case and that's what rubs people the wrong way ... It's very upsetting because he's worked so hard."

She added that she would be "petrified" if a similar scenario had occurred in such close proximity to an inquest into her son's death.

Matthew's father Mark Leveson said he and his wife had communicated with Chief Inspector Jubelin since the claims of misconduct were aired on Thursday evening.

"We told him we were right behind him. He has our unreserved support. I won't address any of the allegations but I willl say, for Matt, he gave his all."

Mr Leveson said "the mind boggled" that the top officer would be taken off the Tyrrell investigation, less than a month before a coronial inquest into the missing toddler.

"You want the person who has been there throughout. It would distressing for me to have him taken off at this point."