Indonesia's military says it has complained about what it believes was discriminatory treatment of its army personnel during an Australian shooting competition last month.

Marksmen from the Indonesian army thrashed competitors in a shooting competition in Victoria, winning 30 gold medals, 16 silver and 10 bronze.

In contrast, Australian army personnel only won four gold, nine silver and six bronze.

Indonesia's army spokesman said his shooters were singled out by the Australian military and were asked to have their weapons dismantled and inspected.

Brigadier general Wuryanto said Indonesia complained because it is not in the rules and no other competitors were asked to present their weapons for inspection.

The annual shooting competition is hosted by the Australian army and was held at Puckapunyal.

It was the eighth consecutive year Indonesia's marksmen have won the overall competition.