Department spokeswoman Sue McKeage says the audit was launched in January after concerns were raised about an employee within the department.
She says the employee was initially suspended with pay, but fired this week.
McKeage declined to discuss the nature of the allegations against the employee, and would not identify the worker.
She would only say that the audit uncovered "irregularities" and the department has asked the RCMP to look into the matter.
RCMP Cpl. Andrew Joyce confirmed the force has launched an investigation, but declined to discuss the probe.