The agency had collected nearly $3 million in fees from about 20,000 applications processed.
Immigration general manager Rob Stevens said the error was only spotted shortly before the email was sent out to the staff.
"During the drafting of the new regulations (for the Immigration Act 2009), the wording of this fee was incorrectly changed from variation of conditions to variation of travel conditions," Mr Stevens said.
"This small change was not noticed at the time because there was a lot of other urgent work happening to ensure the new act went into effect smoothly."
The agency stopped charging the fee when it realised the error.
A variation of conditions was required for migrants on temporary visas, such as work or student visas, when their circumstances changed.
Those wanting a refund will need to complete a refund request form, which can be downloaded from the Immigration website. "It may take several weeks to process the refund," the agency said.