Below is an article published by The Age:

Yonias Siahaya's eyes, wide open and full of fear, shift constantly. They dart from left to right, across the crowded ward at Ambon's main hospital, like those of a wild animal just caught and caged.

Mr Siahaya, 58, is in considerable pain, his left side immobilised from the waist down, his hip fractured, he says, in a savage beating last month by members of Detachment 88, Indonesia's elite counter-terrorism unit funded and trained by Australia and the US.

But the construction worker and father of eight children is not a radical jihadist. He is a Christian, and his crime was to be found in possession of two flags of the Republic of the South Moluccas, the banned emblem of separatists based in and around Ambon, an island in Indonesia's east most famous as the bustling hub of the lucrative spice trade in the 17th and 18th centuries. The Republik Maluku Selatan (RMS) movement claims widespread support but is, by most accounts, small.

All agree it has little or no military capacity. But while it lacks size, it has a knack for launching peaceful protests aimed at embarrassing Indonesian President Susilo Bambang Yudhoyono.

In 2007, a group of RMS activists infiltrated a Family Day ceremony hosted by Dr Yudhoyono at Ambon's Merdeka stadium.

Posing as a dance troupe, they somehow convinced organisers to let them perform the Cakalele war dance before unfurling a nine-metre long RMS flag hidden inside a drum before a stunned and angry Indonesian President.

Mr Siahaya was part of a new plot, this time to float dozens of the distinctive blue, white, green and red coloured flags attached to helium filled balloons during Ambon's Sail Banda regatta in August, when the city was filled with foreigners and Dr Yudhoyono was again visiting.

Mr Siahaya is especially agitated when The Age visits because the police security detail that has been guarding him for more than two weeks have briefly left their posts and could return sooner than anticipated.

He is, however, anxious to tell his story, which begins at 3am on August 2 [date], when police raided his home.

''They took me to the Detachment 88 office in Tantui. There, they blindfolded me and asked me questions,'' he says.

''They didn't believe what I was saying and they started hitting me. They hit me repeatedly … with fists and kicks on my face and body.''

[...]

The allegations add to a growing disquiet about elements of Detachment 88, including its recent propensity to shoot dead a large number of terrorist suspects, foregoing potentially valuable intelligence and giving jihadists a rallying cry against the Indonesian state.

The allegations also raise broader questions about Indonesia's approach to peaceful protest, especially given the recent history of its security forces harshly prosecuting dissenters in Maluku and Papua.

Ahmad Yani, a legislator from the United Development Party (PPP), said Detachment 88's foray into battling separatism and its recent history of using excessive force was ''completely out of their job description''.

He warned that the counter-terrorism unit risked becoming the modern equivalent of Kopassus under the Suharto dictatorship, the Indonesian military's special forces unit that acted with impunity, kidnapping and killing political activists across the archipelago.

''We have to be really careful about it because we don't want anyone to turn the clock back to the old days when Kopassus got training in the US and tortured their own people when [they returned] back home.''

This year, the United States agreed to restore ties with Kopassus that were severed in the late 1990s.

But, as revealed in today's Age, it quietly installed a ban on training Detachment 88 members linked to abuses in Maluku in 2008, a response to the brutal round-up of activists linked to the dance incident in 2007.

That ban, which was not revealed at the time, remains in place, says a spokesman for the US embassy in Jakarta, Paul Belmont. Indeed, The Age understands the ban has been extended to include new members of the unit associated with last month's abuses.

''We have been critical of alleged human rights abuses against separatists, in particular in Papua and Maluku,'' Mr Belmont said.

Australia, too, is deeply concerned.

''The Australian government is aware of, and concerned by, the allegations of brutality towards political prisoners,'' said a spokesman for the Department of Foreign Affairs.

The spokesman declined to confirm or deny whether Australia had introduced a similar ban to the US.

Asked to comment about what's happening in Maluku, the national commander of Detachment 88, Tito Karnavian, was unable to grant an interview but insisted via an ''official statement'' delivered by SMS that ''Det 88 of headquarters that I lead did not deal with that case''.

But the co-ordinator of the Indonesian human rights group Kontras, Haris Azhar, says it defies common sense that Detachment 88 leaders in Jakarta do not know what's happening in Maluku and Papua, where persistent allegations of torture involving its officers have been emanating for three years.

''Jakarta should know what their representatives in local police do. Otherwise, what are they doing in Jakarta?,'' said Mr Haris. ''This is part of the system to limit information to the public.''

Mr Haris said the issue of abuses by Detachment 88 needed to be investigated thoroughly and those responsible for abuses brought to justice, something that has not happened to date.

''This is a serious problem not only for Indonesia but also for donor countries like the US and Australia. They, too, have to be responsible for what Detachment 88 does,'' said Mr Haris.

''Their brutality against the [Malukan] activists, for instance, will nurture the seed of hatred against the country. So Detachment 88 is now a social problem for this country.''

The counter-terrorism force is to be restructured and its dispersed units placed under 10 regional commanders directly answerable to the police chief in Jakarta.

But the new structure still puts a premium on the force combating ''ethno-nationalism'' or separatism.

''Detachment 88 was formed to focus on terrorism but it can also be deployed to counter high-intensity crime, so handling separatism movements is not out of their jurisdiction,'' said Marwoto Soeto, the national police spokesman. Flying flags and floating balloons hardly seems to qualify as a ''high intensity crime''.

But Yonias Siahaya and the others arrested last month can expect long prison sentences if, as expected, they are formally charged with ''makar'', or rebellion, under Indonesia's criminal code.

About 70 people were rounded up after the 2007 dance incident and are now serving sentences of between six and 20 years, more severe punishment than that given to many people charged with serious terrorism and corruption offences.

Yusuf Sapacoli, temporarily out of prison and in the same hospital as Mr Siahaya due to chronic kidney problems he attributes to beatings and being forced to drink hot water infused with carbon paper, was among those arrested in 2007.

''I got 12 years [in prison],'' he says.

''I told the court I didn't commit rebellion. I never carried a gun and pointed it at anyone or anything. I never launched any violent attack against the state. I only wanted to prove that I have the right to express my opinion.''