John McBeth, Jakarta – Indonesia's elite have always preferred to bury unsavoury events, such as those from the bloody upheavals of the mid-1960s. But as much as the Indonesian Armed Forces and other government agencies want to forget the past, human rights campaigners – urged on by the families of victims – continue to demand accountability for dark deeds in the country's not so distant past.

If the signals coming from President Susilo Bambang Yudhoyono's inner circle are any indication, those who have grieved for so long may finally be seeing a glimmer of hope that justice will be served after all.

'This is a new government, this is a new President,' presidential spokesman Andi Mallarangeng told The Straits Times. 'The President is adamant and sincere in wanting to solve these cases.'

Last year's general and presidential elections showed the world that Indonesia is making rapid strides towards a functioning democracy.

But while the military has been edged out of an active role in national politics, some senior retired and active duty officers still feel they are above the law – a special class of people who do not have to answer to anyone because they feel that their actions at the time were in the national interest.

Back during the days of president Suharto's 32-year rule, no one in power ever envisaged the time would come when they would have to turn up and answer questions about their actions.

Now, in a decidedly different era, they are surprised and very much annoyed that civilian investigators are raking over everything – from the 1984 Tanjung Priok shootings to the kidnapping and torture of pro-democracy activists during the dying days of Mr Suharto's rule.

Still, it is an uphill struggle that may eventually require President Yudhoyono's personal intervention. The failure of Indonesian courts to convict a single military officer for the deaths and destruction in then-East Timor in 1999 has set the standard for other human rights cases.

Thanks to a lack of cooperation on the part of the military, the police and even the legislature, the government has made little progress in resolving the matter of the May 1998 sniper killing of four students at Trisakti University as well as the shooting deaths later that year of nine demonstrators in central Jakarta.

It is also no closer to the truth about the riots in 1998 which left hundreds dead and led ultimately to the collapse of the Suharto regime.

Of the 48 government officials called for questioning by the Indonesian Commission on Human Rights in 2003, only three complied. Among those who did not were former armed forces chief Wiranto, current Defence Ministry secretary-general and one-time Jakarta regional commander Lieutenant-General Sjafrie Sjamsoeddin, and the ex-head of the Army Strategic Reserve (Kostrad), Lt-Gen Prabowo Subianto. They are among the handful who know the story behind the violence.

The commission prepared a 1,500-page report on the riots and, in September 2003, forwarded the document to the Attorney-General's Office, with the expectation that it would conduct an investigation of its own. Six months later, however, prosecutors returned the report to the commission, reportedly because it lacked testimony from key members of the military and police – some of the same people who have consistently refused to answer questions about events leading up to the riots.

The commission is now running into similar problems in its efforts to re-open the case of 21 pro-democracy activists who were kidnapped and tortured in a secret south Jakarta detention centre in 1997-1998. Twelve of those abducted are missing and presumed dead, their bodies rumoured to have been buried at sea in concrete-filled drums.

Messrs Wiranto, Prabowo and Sjafrie have all failed to appear to answer questions. Nine other witnesses to be called include Colonel Chairawan, the former commander of Group Four, the clandestine arm of the special forces. Col Chairawan saw his career languish until late last year, when he was controversially appointed to head Aceh's Lhokseumawe district command – the scene of intense operations against separatist Free Aceh Movement guerillas.

Meanwhile, armed forces chief General Endriartono Sutarto had insisted that a recommendation was required from the House of Representatives to give the commission a legal basis for questioning retired and serving military officers because of the non-retroactivity principle inherent in the 1999 Human Rights Law.

But during a recent hearing, the parliamentary commission on legal affairs ordered Gen Endriartono to provide complete access to any information the human rights organisation requires.

In a statement that would have been unheard of a few years ago, the parliamentary commission's deputy chairman, Mr Akil Mochtar, described Gen Endriartono's demand as groundless and accused him of attempting to hinder the investigation.

Mr Akil and civil society groups have all pointed to a number of articles in the 1999 legislation and a subsequent 2000 law establishing Indonesia's first human rights court as giving the human rights commission the authority to question victims, witnesses and other related parties.

Similar obstacles have been thrown up by the National Intelligence Agency, or BIN, in the investigation into last September's bizarre poisoning death of human rights campaigner Munir Said Thalib.

Ex-BIN chief Hendropriyono twice refused a summons from a government-appointed fact-finding team, which was formed in the first place because President Yudhoyono was persuaded that the police could not be relied on to do any heavy lifting if the case lurched into sensitive territory.

Clearly, it now has. A string of phone calls made by an alleged leading suspect to BIN headquarters soon after Mr Munir's death aboard an Amsterdam-bound jetliner raises the possibility of perhaps a link to the agency. The fact-finders, reasonably enough, want to know the nature of those calls. Mr Hendropriyono, who was head of BIN at the time of the murder, and other senior active and retired intelligence officials have been apparently reluctant to enter an environment over which they have little influence or control.

Mr Munir had made some powerful enemies with his vocal criticism of the Indonesian military's human rights record in Aceh and Papua provinces and its involvement in illegal logging and drug smuggling.

Mr Hendropriyono's lawyer, Mr Syamsu Djalal, a former military police commander, underlined that hostility when he told reporters: 'I'm sorry to say this, but who is this Munir anyway that a presidential regulation had to be issued? A lot of people die, but no regulations are ever made (for them).'

That snipe is unlikely to have gone down well at the presidential palace, given Mr Hendropriyono's long history of loyalty to former president Megawati Sukarnoputri, leader of the opposition Indonesian Democratic Party for Struggle.

'No one is above the law,' said the President's spokesman, Mr Mallarangeng. 'If they think that way, they're going to get a surprise. The fact-finding team has been told it will get all the assistance it can get. Anyone who doesn't want to cooperate will have to answer to the President – it's as simple as that.'

Mr Hendropriyono had insisted that Mr Munir was never a target of BIN. But the longer his resistance to the investigation, the more suspicion has focused on the agency. And it appears to be taking its toll.

Asked by Tempo news weekly recently how the public scrutiny had affected him, the retired three-star general replied: 'In a very big way. For instance, here I am hosting a visit by some overseas colleagues. When it came time to drink refreshments, they asked me: 'No arsenic, right?' Of course they were joking, but nevertheless it hurt.'