Eastern Health says the computer software had been up and running since last Wednesday.
The move follows a number of revelations surrounding privacy breaches by employees.
This month it was revealed that the files of 46 patients were inappropriately accessed by two people at a rural clinic and in July, Eastern Health said more than 100 files were accessed by a nurse.
That employee was fired along with four other employees, while another six were suspended.
Authority CEO Vicki Kaminski says the privacy rules are clear there is no tolerance for wilful breaches of privacy.