Suppress a powerful internal military revolt - and quite probably run the risk of provoking a military coup - or continue as present and risk becoming as much of an international military pariah as the Serbian army?
The choices faced by those at the top of the Indonesian military are not easily made, but they must be made fast.
The Indonesian military is larger than New Zealand’s total population. It is spread over a nation of 15,000 islands and more than 100 languages. It is used to getting its own way and it is used to exploitng its might to economic advantage. It is used to suppressing rebellions. It is not used to retreating, withdrawing or handing over its responsibilities to international peace-keepers.
Possibly most importantly, the Indonesian armed forces have a tradition of political involvement and of considering themselves the loyal servants of the Indonesian people.
Speaking in Jakarta this morning senior commander Brigadier General Sudjarat told the BBC that a new commanding officer has been appointed to oversee the operation in East Timor. This is a positive development, but it is difficult to discern what exactly it means.
At the same time Jakarta is rife with rumours of a meeting between the Indonesian President and his Generals and a possible coup.
In the interview General Sudjarat, true to form, refused to concede that the situation was out of control in East Timor. “We have imposed a military state of emergency in East Timor,” he said. “That is why we have appointed a new commanding officer to restore law and order in East Timor.
To questions on whether he thought the situation out of control he replied: “I think the Indonesian government still has control in East Timor and the whole country. We have more access than the people of the UN have in East Timor.”
In this final comment General Sudjarat is certainly right – there are no longer very many reliable reports, indeed many reports at all, arriving from independent sources on the ground in East Timor.
Hopefully he is also right that the new appointment may make a difference.
Indonesian complaints about the running of the UN referendum do have some basis. They in no way justify the response of military units in East Timor but they do go some way towards explaining them.
With the benefit of hindsight it is clear that the referendum was mishandled. Apart from being at the wrong time, during a period of political uncertainty at the centre of the huge Indonesian republic, it was also insensitively and clumsily handled. The British and Irish do not approve plebescites in Northern Ireland unless they have first dotted the I’s and crossed the T’s with all the participating parties. This was not achieved in East Timor, and warnings were ignored.
On the other hand Indonesia too is far from free from blame. Indonesia consented to the election and promised to keep order – promises it has failed spectacularly to fulfill.
Now the Indonesian military has to consider its options. It could – as has been rumored this morning – conduct a coup, replace Habibe, role back democracy in Indonesia and continue to wreck mayhem in East Timor.
But if it does this it has a lot to lose. In the short term it will quickly see its proud reputation – which is already being rapidly dulled – dashed absolutely. It would quickly become a military pariah unwelcome to exercise and train with forces from the West and possibly even inside ASEAN.
It’s commanders could be, and if something does not happen soon, probably will be, indicted for war crimes. In the process the recovering economy in Indonesia would probably be cast back into the whole it was in last year.
But most significantly if it chooses this path it runs the risk of losing the respect of the Indonesian people whom it has sworn to defend.
Indonesia has embraced democracy with some enthusiasm. This has meant already considerable change for the Indonesian military. Following events during Indonesia’s transition to democracy the Indonesian military found itself for the first time subject to independent judicial investigation.
As the process continues the military will have to continue to give up more of the vestiges of wealth and power that it has ascribed to itself when it was the only law.
Now however Indonesia has a free press, it has a free opposition, the military’s power in the new Parliamentary assembly has been diminished. And Indonesians will not now willingly go back to the bad old days.
While anti-foreign interference rhetoric may be firing up the audiences in Jakarta today and yesterday, it is only a matter of time before the Indonesian public realises that the brutality and callousness shown by soldiers in East Timor could equally easily be applied to them.
By pursuing law and order in East Timor the Indonesian military can secure its continued presence at the top table of Indonesian influence for decades to come. By pursuing a path of anarchy, deceit and treachery it assures only its eventual destruction, in both the short term and the long term.
Really it is a matter of self preservation. And maybe, in those terms, it is not quite such a hard choice afterall. And if the chouce turns out to be a wise one - those who made it could well find themselves written into the history books as heroes.