Lawyers representing the four educators told the Queanbeyan Local Court on Tuesday their clients are pleading not guilty.
Police allege the boys aged nine, 10 and 11 were assaulted at their Queanbeyan school between January 2024 and December 2025.
The principal of the school, which cannot be named for legal reasons, in addition to a 65-year-old woman and a 38-year-old man have each been charged with one count of common assault.
Another man, aged 46, is facing three counts of common assault.
None of the four teachers are currently working at the school and they did not attend the first court hearing.
The case will return to court in early June.
Detectives launched an investigation in November with help from officers at the Department of Community Justice and Department of Education.
It led to the four staff members being charged by police.
In a previous statement, the education department said while the exact nature of the assaults was not known the allegations were deeply concerning.
"Behaviour of this kind is unacceptable in any school," a spokesperson said.
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