Australia's agriculture sector is facing another headache in Indonesia, just weeks after it had lost the battle to Pakistan which culled 21,000 Aussie sheep.

This time, the problem is the Indonesian Customs had held up shipment of $10 million worth of Australian beef which remain at a Jakarta port due to alleged anomalies with the import documentation made by the Indonesian importer.

The hold order covers not only Australian beef but also shipments from other countries. To worsen the situation, key Indonesian officials who could decide on the matter are all out of the country participating in the Hajj pilgrimage to Mecca, Saudi Arabia.

Another headache for the importer as well as the exporter is the ballooning port charges on the shipment.

Among the solutions being eyed by the Australia's Department of Agriculture, Fisheries and Forestry are to expedite the processing of the documents or re-export the beef to another market. However, it may end up with a fate similar to the Aussie sheep which were initially rejected by Bahrain but accepted by Pakistan, only to be culled later.

Agriculture Minister Joe Ludwig has written to his Indonesian counterpart, Agriculture Minister Suswono to seek an early solution to the problem.

It is not the first time that Australia encountered problems with beef shipments to Indonesia. The Agriculture Department had previously banned export of live animals to Indonesia because of the inhumane and brutal way the animals are slaughtered based on videos taken by animal rights groups in the Asian country's abattoirs.