Analysis: Indonesia's special forcesIndonesia's military has been closely associated with the militias
By BBC News Online's Julian Duplain
The Indonesian military has denied that around 10 soldiers detained by Australian peacekeepers on Tuesday are members of Kopassus, the Indonesian army's special elite unit.
The men were detained as militia suspects, but some of them were found to be carrying Kopassus identity cards. There are close links between Kopassus and the pro-Jakarta militias responsible for the violence after the vote in favour of independence on 30 August.
Radio messages intercepted by observers from the International Federation for East Timor demonstrated how Kopassus commanders liaised with the militias at the time of the vote.
Kopassus commanders were heard giving instructions to militias to start trouble, intimidate observers and block roads. They also cautioned the militias to try not to appear to initiate any clashes.
Kopassus units have also been active in other ethnic troublespots, such as Aceh and West Papua.
They have received training in the US, the UK and Australia.
Kopassus were the crack troops of former Indonesian President Suharto, and are believed to have been behind many covert operations during his 32-year rule.
These included the 1997 abduction of a number of anti-government activists, several of whom are still missing.
Seven middle-ranking Kopassus officers were arrested a year later in connection with the case, but the unit continued to operate unchecked.
Suharto's son-in-law, General Prabowo Subianto, was a long-time Kopassus commander and was a senior military officer in East Timor at one stage.
He was dismissed from the military after last year's anti-government riots in Jakarta, which triggered Suharto's downfall.
Former General Prabowo was among those Kopassus commanders who received training in the US.
General Kiki Syahnakri - who was in charge of East Timor under martial law immediately after the independence vote until handing over to international peacekeepers on Monday - was another.
After a November 1991 massacre of East Timores peasants, the US Congress restricted military aid to Indonesia, but continued to train special forces.
Since then, US special operations forces have conducted 41 training exercises - most involving Kopassus - covering counterinsurgency techniques, psychological warfare, urban operations and "internal defence".
Kopassus troops were also trained in the UK, where seven members completed a course at Hull University last summer.
In May 1998, US officials decided that Kopassus had been involved in torturing political dissidents.
But in the past week Pentagon officials have maintained that without US training for Kopassus troops, the situation in East Timor might be worse. "You don't fix them overnight, but you at least stand a chance if you've got people in there talking to them and people living in America looking at how we operate in this society," said an official quoted by the Washington Post.