Indonesia will only allow 50,000 head of cattle between July and September this year, down from 250,000 the previous quarter.

The Australian Livestock Exporters Council chief executive Alison Penfold told ABC radio on Tuesday the quota reduction is significantly below expectations, and has taken the industry by surprise.

Ms Penfold said 50,000 was "clearly not very much".

"We'll have to work our way through and hope the figure bounces back," she said.

Exporters are unsure what prompted the decision, which was only taken last week.

But they do not believe any political reasons are behind it.

"I think people are suggesting there are a whole range of issues that are related - that's not our view," Ms Penfold said.