While the military was forced to surrender its considerable political clout in the late 1990s, as democracy, and political parties, returned to power, the generals and professional military have not changed their attitudes (condescending) towards politicians, and civilians in general. The military officers consider themselves more disciplined and competent to run the country. But the generals are as corrupt as the civilian politicians. The generals simply believe that they are more deserving of what they steal. Anti-corruption efforts are believed to be more theater than substance. Some people have been convicted, but a lot of the biggest crooks tend to get off, or simply get out of the country.
Decades of corruption in the military has left the troops with a lot of obsolete and, quite often, inoperable (because maintenance funds have been stolen) equipment. Billions are now being allocated for new weapons and equipment, and it's widely believed that these new purchases will involve the usual corruption. For example, three CN235-220 maritime reconnaissance aircraft were just ordered, costing over $25 million each, and it's believed that these new aircraft will stay on the ground (which allows operating and maintenance money to be stolen) nearly as much as the obsolete aircraft they are replacing. Time will tell.
In neighboring Malaysia, Moslems (who are 60 percent of the population) are rioting and destroying Christian churches, because courts declared it legal for Christians to call God Allah in their publications. The reason for the ruling is that the use of Allah as the term for a Christian God predates Islam (especially in Egypt, where the Christian Copts still use the term). But Islamic conservatives believe that Moslems now "own" the term and are willing to use violence to defend that belief.
January 8, 2010: In Papua, two tribes fought over money and rape, leaving one man dead and over a dozen wounded. Such disputes are common, because the Indonesians don't have much of a justice system in many parts of the province, and the locals don't trust the Malay officials the government sends to run the police and courts.
January 2, 2010: Police arrested four women for putting on a New Years eve show that involved taking their clothes off, thus violating the new anti-pornography laws. It was believed that these laws would be used to outlaw anything a cleric declared was un-Islamic. Strippers are nothing new in Indonesia, but Islamic conservatives have always complained that such behavior was corruption from the West and wrong. The clerics are also protesting, without saying it, bawdy customs that pre-date Islam in Indonesia, and just won't go away.
January 1, 2010: In East Timor, the local police force (some 3,000 recently recruited and trained personnel, and 1,500 UN police advisors and instructors) has, over the last month, taken over responsibility for security throughout most of the country. There are doubts that the police are yet professional enough to be left on their own. The government has no income to speak of, and depends on foreign aid to meet the payroll and keep the lights on. The economy is minimal and unemployment is over 30 percent.
December 25, 2009: In the two weeks leading up to Christmas, Islamic conservative groups organized dozens of attacks on Christians, and their churches, mostly in Java. This happens every few years, and this year the government mobilized 11,000 troops to protect Christians during Christmas. Christians are a minority nationwide, while 87 percent of the population is Moslem. The tensions in places like Sulawesi are not entirely religious. The Christian areas used to be almost entirely Christian, but over the last three decades, the government has encouraged (with laws, money and land) Moslems from overpopulated areas, to move to less populated Christian areas. This has created frictions, which some Islamic clerics exploit.
There are also problems in West Timor, where many Malays who fled in the 1990s, when East Timor became independent, have not gotten along well with long-time West Timor residents.
December 19, 2009: In Papua, hundreds demonstrated to protest the police killing of separatist leader Kelly Kwalik separatist leader Kelly Kwalik.
December 17, 2009: In Papua, separatist leader Kelly Kwalik was killed by police, who had gone to arrest him in the middle of the night. Kwalik was accused of being behind a series of shooting outside a mining complex earlier this year, but no proof has been presented. Kwalik was also believed involved in a shooting in 2002 and kidnappings in 1996.