According to local reports 50 firefighters were battling the blaze, which broke out on the patrol boat HMAS Bundaberg at 1152hrs local time.
Pictures from 7News TV channel showed smoke billowing from the boat shed across the Brisbane skyline.
The HMAS Bundaberg is a 2007-built 56 m patrol vessel and was under repair in a facility in Brisbane Marine Industry Park.
Local reports said one man was treated for smoke inhalation but no other injuries were reported.
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