From 1 January, a new, non-refundable fee of $3,000 will be payable when applying for a warehouse licence.
The increased fee comes as a result of a comprehensive review of licensing costs that was undertaken by the Department of Immigration and Border Protection (DIBP) in August and September.
In addition to the $3,000 application fee, licencees will also be required to pay a $300 fee for requests to change a warehouse licence.
A spokesperson for the department said: "DIBP undertook stakeholder engagement sessions during August and September 2015 looking at four different options, with the final decision made by DIBP and the relevant Bills passing through Parliament during November 2015.
"The review found that DIBP have three licence types where charges were misaligned. The Fees Review identified ways in which charges could be aligned across all licence types."
The notice of change, including a full list of fees can be found on the department's website.
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