The army is cracking down on undisciplined soldiers, who often create problems with locals. The lack of discipline often results in brawls with local civilians and police. Soldiers will rob and assault civilians while off duty, even when they are closely supervised while on duty. In the Malukuks, 56 soldiers were thrown out of the army. However, only 12 went through court proceedings, the other 44 had deserted when they found themselves under investigation. Desertion is another problem, with thousands of soldiers just walking away each year.  Similar prosecutions are taking place in Aceh.

The crackdown on bad behavior goes along with an attempt to root out corruption in general. This has led to some prosecutions, but it has also created a backlash, with prosecutors being threatened, and bribes offered to back off on investigations.