The Morrison government has quietly increased the fees imposed on arriving cargo ships and planes and, in another year, will apply a new levy to importers, all of which will be used to fund the nation's spiralling biosecurity costs.

Federal Agriculture Minister Bridget McKenzie has outlined the new two-step process after officially dumping a biosecurity levy that was proposed in the 2018 budget but fiercely opposed on the basis it was ill-designed, poorly-thought through and deemed unworkable.