Ian MacKenzie, Jakarta – Indonesia's armed forces, who have traditionally regarded themselves as the defenders of the country's unity and stability, are under unprecedented fire as they emerge from the shadow of the former president Suharto's regime. Last week was a black one for the armed forces, known by the acronym ABRI:

An investigation opened into the possible involvement of the former commander of the elite Special Forces (Kopassus), Lieutenant-General Prabowo Subianto who is Suharto's son-in-law, and two other senior officers in the kidnapping and torture of political activists;

An army investigation identified eight soldiers as suspects in the fatal shooting last month of a student during a pro-independence rally in the remote eastern province of Irian Jaya;

Mass graves were reported in the far western province of Aceh on Sumatra island amid accusations of army atrocities in quelling a separatist insurgency in the early 1990s.

"ABRI is in a very difficult position because of the uncovering of many misdeeds during the time ABRI was under Suharto," political commentator and military historian Salim Said told Reuters. "It seems that society now is demanding clarity of response from ABRI as to why this kind of thing happened in the past."

Said and military sources place the blame for the behaviour of the military on Suharto himself, and on a polarising Cold War rigidly anti-communist ethos which is only now starting to dissipate.

Suharto himself resigned on May 21 and was replaced by his vice-president B.J. Habibie after riots jolted Jakarta and other major centres amid a crippling economic crisis and mounting demands for political reforms. "The armed forces were really used by the Suharto regime to maintain and perpetuate his own power over the past 32 years," said Salim Said said.

ABRI commander General Wiranto, a former Suharto aide who is regarded as a highly professional soldier widely respected among the military, has been shuttling around the sprawling archipelago in a bid to control the damage. In Aceh on Friday, he ordered an end to a decade-old military operation and the withdrawal of combat troops – and publicly apologised for any suffering its 3.5 million people may have experienced in army hands.

On Saturday, Wiranto – who is also defence minister – was in the central Javanese city of Solo appealing to the people to help the military ensure security and stability. "Security is not the responsibility of ABRI alone. Security is the responsibility of all the people of Indonesia," he said.

Foreign military observers say the size of the armed forces is relatively small and thinly spread in a country as vast as Indonesia – some 17,500 islands stretched for 5,000 km (3,120 miles) along the equator. The London-based International Institute for Strategic Studies puts the size of the armed forces at 461,000, a figure that includes 177,000 police who are technically under ABRI.

ABRI has also started to withdraw troops from East Timor, a running sore in the side of Indonesia's international relations since it invaded the former Portuguese colony in 1975 and annexed it the following year. The invasion came after Portugal abandoned the territory. President Habibie has offered East Timor's 800,000 people a wide measure of autonomy and talks on its future now are finally taking shape.

Military sources say ABRI, which had regarded the territory as its particular fiefdom and a source of combat experience and medals fighting an insurgency, is now ready to quit an arena that no longer provided any distinction.

Political and military analysts say ABRI now is unpopular in many parts of the country, partially due to its dramatic failure to prevent or halt the May riots, in which at least 1,200 people died in Jakarta alone, and to its association with the corruption and nepotism of the Suharto era. Military sources say morale is very low, within the army at least, a victim of low pay aggravated by the nation's devastating economic crisis, and by the anger of ordinary people.

Suharto himself was commander of the Kostrad special reserve, the army's main combat force, during an abortive coup attempt blamed on the now-banned Communist Party of Indonesia (PKI) in 1965. He used the coup and its violent aftermath to take power from the country's late founding president Sukarno and consolidate his position as the country's leader for the following three decades. He carefully manipulated ABRI promotions and postings to his own ends.

Thousands of PKI members were killed or thrown into jail, where some still languish. Political sources said any hint of a communist revival brought down the heavy hand of military intelligence on the suspects in a rigid Cold War response.

At the same time, some sources say, the military was equally fearful of any rise in Islamic fundamentalism and the extreme right that might endanger the unity of a disparate nation of 200 million people made up of some 300 distinctive ethnic groups.

The ghosts of the past are likely to haunt the military for years to come unless Wiranto can make a radical break with the years under Suharto.

ABRI has consistently been accused of killings, torture and other human rights abuses in its areas of operation, particularly East Timor, Aceh and Irian Jaya. "Wiranto is in a very difficult position in how to deal with all these simultaneously," said Salim Said. "Wiranto should make it clear that what happened in the past, that the force used by the (Suharto) regime to victimise its own people, was wrong, and that such a thing will never happen again," he said.