William Tyrrell's foster mother will plead not guilty to giving misleading or false evidence to the NSW Crime Commission.
The charges against the 56-year-old woman, who cannot be identified, are in relation to evidence she gave during a hearing into William's disappearance from his foster grandmother's home on the Mid North Coast in 2014.
The NSW Crime Commission works alongside NSW Police and can hold hearings and supply evidence to courts to facilitate prosecutions.
The maximum sentence for misleading the body is five years imprisonment.
Neither the foster mother nor her lawyer appeared at Sydney's Downing Centre on Tuesday, with correspondence submitted electronically to the court indicating she would plead not guilty.
However, a police informant involved with the case attended and sat in the public gallery.
Earlier this year, William's foster father, who cannot be named, also pleaded not guilty to two charges of giving false or misleading evidence to the crime commission.
The 55-year-old will front court for a two-day hearing in October where audio recordings of his police interviews will be played.
Last year, both foster parents were charged with the alleged common assault of a child at a home on Sydney's north shore.
The child is not William.
The specific allegations relating to the assault are suppressed but the pair have pleaded not guilty.
Following further investigations by detectives from Strike Force Rosann, which was established to probe William's disappearance, the foster mother was hit by another assault charge in February.
The foster mother's lawyers have already indicated she will seek to have her assault charges heard under the Mental Health Act.
Despite a $1 million reward and hundreds of persons of interest being interviewed, no one has ever been arrested or charged over William's disappearance.
Late last year police investigators conducted a fresh search around the Kendall home where the three-year-old was last seen.
Although the foster mother was initially ruled out as a suspect, she became a person of interest for a period of time last year.
There have been about 600 persons of interest over the past seven years.
The foster mother's charges relating to false evidence will return to court on June 7.
