The processes of justice in Indonesia's court system continue to baffle anyone looking for consistency or punishments fitting the crime.

A well-connected member of the Jakarta elite, especially someone belonging to top military or crony circles around the former president Soeharto, can expect to spend a comparatively short time in jail, whatever the crime.

An offender from the lower social orders, or a foreigner, can expect draconian punishment, increased rather than lessened on appeal.

So it has been with Tommy Soeharto, perhaps the most egregious of the former president's children in greedy rent-seeking during his father's 32-year rule. A Jakarta judge gave Tommy an 18-month jail term in September 2000 for a real estate deal that ripped off the state food agency. This was eventually overturned on appeal, but by then Tommy had organised the judge's murder from the Jakarta safe houses where he had hidden from justice. After a year on the lam, Tommy was arrested and in September 2002 sentenced to 15 years in jail for the judge's murder.

A sentence cut of five years followed, and with cumulative remissions for good behaviour Tommy has walked free, having spent just five years in custody. He returns to enjoy the wealth of his Humpuss group, still plugged leech-like into the state oil company, and estimated variously to be worth between $US250 million and $US1 billion.

Another beneficiary of Indonesian clemency has been Pollycarpus Budihari Priyanto, given 14 years in jail late last year for administering a lethal dose of arsenic to the human rights lawyer Munir Said Thalib while sitting next to him on a Garuda Airlines flight. His main sentence has just been annulled by a higher court, leaving a minor accessory conviction drawing two years' jail, which will have been served in a few months.

The riddle of what Pollycarpus, an off-duty Garuda pilot, had against Munir is still unexplained – as are the 41 calls logged on his mobile phone to a deputy chief of the State Intelligence Agency. Munir's courageous work in exposing the Indonesian military's crimes against humanity in East Timor suggest a motive.

The clemency perversely shown in these murder cases, and to some involved in the Bali terrorist bombings, will make it harder for Australians to accept the more severe sentences meted out to drug smugglers and the wildly divergent sentencing patterns of different judges and courts. It will raise more questions about co-operation with Indonesian police and intelligence agencies. It will increase expectations that political pressure on Jakarta can influence sentencing and commutation decisions.