The live animal export industry is furious the Federal Government is raising fees for certification and inspection by more than 60 per cent.

Industry body the Australian Livestock Exporters' Council has labelled the fee hike an "act of bureaucratic bastardry", and says it may send some exporting companies broke.

The council's Alison Penfold says the move is simply revenue raising, and is calling on Agriculture Minister Barnaby Joyce to show his support for the industry.

"We see the decision today as an act of bureaucratic bastardry in a race to fix the Department of Agriculture's bottom line," she said.

"We've got exporters facing a per-hour charge of $671.80 for simple document processing.

"There is no reason or rationality to be charging exporters that sort of fee when they are charging other industries far lower amounts on a per-hour basis."

The Department of Agriculture spends about $10 million a year certifying live animal export shipments and making sure welfare is maintained through the supply chain.

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But it only recovers about $6.5 million from industry to perform those services.

In a statement, the department says that shortfall has caused budgetary problems, and in order to give shipments the tick of approval, it needs to recover fees.

Calls for Joyce to take action

Ms Penfold says the industry has done all it can to reduce costs, but the department has not.

"For the last several years we have been ... trying to work with the Government to address the significant inefficiencies in service delivery and have faced bureaucratic stonewalling at each point," she said.

Ms Penfold is calling on Mr Joyce to help resolve the situation.

"The serious issue yet to be addressed by the Minister are these regulatory costs."

Shadow minister for Agriculture, Joel Fitzgibbon, is also insisting Mr Joyce take action.

"If [he] sits back and accepts this, it will be totally inconsistent with what he said about the live trade industry since taking office," he said.

"He's constantly claiming credit for, as he says, getting the live trade industry going again, where in fact it was Labor's work prior to the election that bolstered our output."

Mr Fitzgibbon acknowledges "the difficult period" triggered by Labor's decision to ban live exports to Indonesia but says it has brought about positive change in animal treatment.

"I've said many times that I regret the impact on the industry but at the same time, it allowed us to implement the best animal welfare system in the world - something Barnaby Joyce now always cites when a new export market is opened," he said.

The Agriculture Minister was unavailable for interview but is expected to make an announcement regarding the issue early next week.