On the eastern island of Flores, police and the army have battled repeatedly in the streets of the main city, Maumere. Protection money has emerged as a possible motive for the attack on 10 teachers at the American-owned Freeport Mine in Papua in August, in which two Americans and one Indonesian died.
According to Marcus Mietzner, a German scholar researching the Indonesian military for a doctorate at the Australian National University, some companies are paying protection money to as many as 14 groups, including army, police, ethnic militias and the "security units" or Satgas attached to political parties.
"It has become a very crowded protection sector," Mietzner said. "This is why they are getting more and more desperate and why they are crossing lines they have not crossed before. Why they are killing police officers and probably even foreigners."
This doesn't mean that the security forces would carry out a giant atrocity like the Bali bombings. For one thing, Mietzner points out, the military has direct investments in Bali like the giant Nusa Dua resort, hotels and golf courses, as well as extracting protection money from other tourism operators.
For another, the TNI is no longer under threat from the reform push that two years ago seemed likely to wind up the territorial commands. That pressure has all but vanished since the TNI-friendly Megawati Soekarnoputri took over the Indonesian presidency in August last year and the September 11 attacks made the US worry more about security than human rights or corruption".
There is little reason for the TNI to be dissatisfied with the current situation," Mietzner says. "Everything [has been] going their way."
But it does mean that the Indonesian security apparatus is not much of a barrier to serious terrorists. A determined terrorist with enough money can buy his way in and out of the country and acquire all the explosives and weapons he needs.
The security forces are also in disarray at the top. With vacillating leadership from President Megawati and her top security minister, former general Susilo Bambang Yudhoyono, the chiefs of the various security agencies are busy competing for control of the massive investigation to catch the Bali bombers.
As well as the police team working with the Australian Federal Police, FBI and other foreign experts in Bali, separate investigations are being run by BIN's civilian intelligence agents and by the army intelligence arm called BAIS.
Throughout the investigation, they have made wildly conflicting claims about their progress. BIN's spokesman claimed a week ago that the agency knew the identity of three of the 10 suspected bombers, a claim the police said was a mystery to them.
Since the bombings, the Howard Government has said it wants closer contact with Indonesian security. The US Government has said the same. The problem is that many of the Indonesian security chiefs have themselves organised large-scale violent activities, such as the "Laskar Jihad" (Holy War Warrior) campaign against Christian communities in eastern Indonesia and the anti-independence militias in East Timor.
The unit best prepared for anti-terrorism duty is the notorious army special forces command known as Kopassus, responsible for extensive assassinations of government opponents.
"Any government that sees the TNI or indeed BIN as a solution to the terrorist problem has got to look really carefully at what these people have done in the past, and what they may be doing now," says Sidney Jones, Indonesia director of the International Crisis Group, a Brussels-based privately funded monitoring body.
Since BIN handed over the wanted al-Qaeda operative Omar al-Faruq to the CIA in June, American officials have seemed prepared to overlook the controversial career of BIN chief Hendropriyono.
This week's presidential decree making BIN the co-ordinator of counter-terror operations - involving personnel from each armed service, police and the allegedly less-tainted Unit 81 of Kopassus - may open the way for foreign forces to bypass the politically untouchable Kopassus.
But experts such as Mietzner call this a "quick fix" which will achieve very little. He argues the only way to lift the quality of Indonesia's security forces is to address the problem of military finances, by insisting on full transparency and accountability and possibly considering international aid for the transition.
That may be a multi-billion-dollar program. But as long as the TNI is selffunded, it is outside the Indonesian Government's control and inherently corruptible, and there will continue to be a huge gap in the region's security.
"If you just pump money and resources into the existing system you just perpetuate what is already there," says Mietzner.
TNI, BRIMOB AND STATE TERROR IN THE MOLUCCAS < Back to
The armed forces, or TNI (Tentara Nasional Indonesia), still largely fund themselves from a mix of legal and illegal business activities that raise an estimated $6.4 billion a year.
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