Australia's leading freight and trade organisation says the government is shifting the cost of biosecurity to importers, without increased efficiency in processing documentation.
Agriculture Minister Murray Watt said importers contributed $51 million more to biosecurity operations in just six weeks, since the government moved to full cost recovery.
Mr Watt said the government was delivering stronger biosecurity for the agricultural sector.
But Freight and Trade Alliance director Paul Zalai said while importers were paying more, processing of Full Import Declaration (FID) document assessment times were blowing out.
"The agricultural sector and the National Farmers Federation have been putting a lot of pressure on the minister to get funding through the risk creators, the importers, and we get that," Mr Zalai said.
"We can even live with that, but really, what we are saying is we need an improved service - not only are costs increasing for importers, but service is deteriorating.
"While trying to appease farmers, the minister is frustrating the international trade sector."
The FTA represents organisations such as the Australian Cotton Shippers' Association, the Australian Council of Wool Exporters & Processors, the Australian Meat Industry Council, the Australian Dairy Products Federation and the Australian Horticulture Exporters and Importers Association.
The FID system was very outdated and labour-intensive, Mr Zalai said.
"We still have quarantine officers physically assessing documentation and then making a decision if further inspection is required - those processes haven't changed, in my experience, over the last 40 years.
"When I was a young guy with a full head of hair, I used to go to a quarantine counter with a bundle of documents - the difference now is those documents are scanned, converted to a PDF and sent to the quarantine officers."
Border Force could process documents "within minutes" he said.
"We are waiting days - one of our members had a consignment brought in by airfreight, and was expecting quick release, and they have had to wait six days for the documents to be assessed."
The Department of Agriculture, Fisheries and Forestry had historically addressed peaks in backlogs in import document processing by deploying officers on over-time, Mr Zalai said.
"During the year, advice has been received that due to budgetary constraints, this remedy will not again be used.
"This leaves importers with a remaining option to individually request overtime, which will come at yet another additional cost, above and beyond already high cost recovery fees."
He said FTA had no argument with effectively managing import biosecurity risks and was prepared to pay.
But cost recovery fees were increasing without a commensurate improvement in services.
"We understand and really support a strong biosecurity system." he said.
"I am not quite sure why processing has slowed down.
"We had similar experiences during the pandemic, and that was understandable because of large import volumes and the department obviously had difficulties with lockdowns and things like that.
"We don't really understand why we have got those delays now.
Trade volumes had dropped and working conditions were back to normal," he said.
"They are not coping now, with the low volumes."
He said the FTA was happy with the $5 increase in the cost of import declarations.
"To me, I think that's a fairly modest increase - what we said to the department, at the time, was make it $10, but make sure you deliver a service."
The government has been contacted for comment.