In Central Aceh, the TNI has an ethnic Javanese and Gayo militia force that is estimated to be larger than the Aceh-wide GAM. An investigator who speaks the local Gayo language puts their strength at 12,000 people and 6,000 weapons -- some homemade, some military issue. The Helsinki Memorandum of Understanding (MOU) between Indonesia and GAM has a clause (4.9) for the "decommissioning of all illegal arms" but only those held by "illegal groups and parties," and under Indonesian law state-organized militias can be construed as legal.
Arms held by the TNI - POLRI are, of course, implicitly defined as legal, a privilege which every country in the world grants to its security forces. Some theorists say that the very definition of a state is its monopoly on legitimate violence. So the state's arms are always legal, even if routinely used for illegal acts like murder and theft, or to carry out policies like illegal invasions or occupations.