Shawn Donnan – Indonesian human rights activist Munir had plenty of powerful enemies. As an outspoken critic of the former Suharto regime and institutions such as the military, he had become so accustomed to death threats, friends say, that he long ago stopped counting them.

But when the Dutch authorities revealed last month that his death aboard a flight to Amsterdam on September 7 was the result of arsenic poisoning, it brought back ugly memories of the political assassinations and kidnappings of President Suharto's so-called "New Order".

The apparent murder of the activist (who, like many Indonesians went by one name) also reflects the continuing, and often awkward, transition to democracy in the world's largest Muslim nation.

In the six years since the end of President Suharto's 32-year rule Indonesians have become used to the kind of pugnacious activism and rowdy free press that democracy brings to the fore. Yet many of the institutions and people who propped up the Suharto regime – or built fortunes on the back of its rent-seeking culture – remain powerful.

"Overall, Indonesia is going more in the right direction than in the wrong one," says Sidney Jones, a long-time Indonesia watcher who was expelled by Jakarta earlier this year after her warts-and-all analysis of the country for the International Crisis Group.

"But it's a huge mistake to think you can overcome 32 years of authoritarianism in five or six years," she says. "There are a lot of institutions and individuals within those institutions who are committed to keeping the old order in place."

Indonesia police have begun investigation but who was responsible for Munir's death remains a mystery.

Some of Munir's colleagues have blamed a "powerful institution" for his death, thinly veiled code for the security forces. Much of the initial investigation has also focused on an employee of Garuda, Indonesia's national airline, with apparent links to the former commander of a pro-Jakarta, military-supported militia involved in the 1999 violence in East Timor.

But Munir was also reportedly investigating a high-profile corruption case, so the military is not necessarily the logical suspect. "They [the military] arrest and they frighten and they try to intimidate," says Ms Jones. "But there are very few examples of them actually killing activists."

Rights activists nonetheless view Munir's apparent murder with foreboding. "If even people as famous as Munir are being assassinated, what is going to happen to those of us who work in conflict areas? We have no protection at all," says Syarifah Murlina, a human rights lawyer in the western province of Aceh, where Jakarta has been battling separatist rebels.

But if it has brought back memories of the Suharto years, Munir's death has also highlighted the rising influence of activist groups since his fall.

President Susilo Bambang Yudhoyono, a retired general who took office in October promising to create a "more just" Indonesia, received Munir's widow at the presidential palace and ordered an independent inquiry, although he later backed away from this.

Munir's death has also drawn intense media interest. His face appeared on the cover of the respected Tempo news weekly two weeks in a row and the investigation has been a nightly fixture on news bulletins, prompting one commentator to declare him "even more present in death than he was in life".

But the new-found activist power is not all positive – especially from the perspective of those foreign companies that venture into what many see as a hostile Indonesian investment climate.

A scrappy coalition of environmental activists, for example, has this year accused Newmont, the world's largest gold producer, of causing health problems among local villagers living byabay into which it dumps treated waste, in accordance with its government licence.

Independent studies by the World Health Organisation and others have exonerated Newmont of any wrongdoing at its Minahasa Raya mine in North Sulawesi. The mine was shut, as scheduled, in August. But intense public pressure has forced police to pursue cases against six Newmont managers – including three expatriates – who now face up to 15 years in prison on environmental charges.

Government ministers have made clear that the case has become a political hot potato they would rather let the courts resolve.

Wayne Murdy, Newmont's CEO, admitted recently that his company had been outplayed by local environmental groups, leaving it facing what could be a protracted legal battle. That, he says was a "tremendous statement for freedom" in Indonesia. But freedom also has its costs. "Our reputation has been tarnished by this," he says. "And our reputation is very important."

[Additional reporting by Taufan Hidayat.]