Army spokesman Maj Gen Wuryanto said the halt came into force in December and a broad range of activities were affected, including joint training.
Australian Defence officials confirmed Indonesia had halted all defence co-operation over "teaching materials".
Bilateral relations have been tense at times in recent years, although there were recent signs of improvement.
"All forms of co-operation with the Australian military, including joint training, have been temporarily withheld. I hope it can be resolved as soon as possible," Maj Gen Wuryanto said.