Shanti Krishnasamy, 39, is accused of amending the answer scripts with intent to deceive the markers of the papers into believing that the answers came from the pupils.
It is believed to be the first such case.
The alleged offences took place in Canberra Primary School on Oct 5, where she was invigilating the examination.
She is alleged to have gone through the three pupils' answer scripts and made changes in them to improve the answers before submitting them to her supervisor.
Shanti, who is represented by Mr Anand Nalachandran, is out on $10,000 bail. Her passport has been impounded, and a pre-trial conference has been fixed for Feb 20.
If convicted, she could be jailed up to seven years and fined for each count.
