Indonesia is imposing a new 5% tariff on some imports of live cattle from Australia.
Exporters want the federal government to question if the tariff breaches the free trade agreement signed between Australia, New Zealand and South-East Asian countries.
The Australian Livestock Exporters Council says exporters first heard about the new tariff last month, but it was confirmed during a visit to Indonesia last week.
Chief executive Alison Penfold says it is not clear why the tariff is being introduced, but she thinks it is unlikely to be linked to a live export ban imposed last year after disclosures about cruelty in Indonesian abattoirs.
Importers have now started to receive invoices for the payment of the backdated to about April.
The Indonesian government has confirmed that this year's imports quota will be significantly lower than last year, with a total of 283,000 permits issued.