After weeks of manoeuvring behind the scenes at the United Nations, it has become clear that if East Timor votes for independence - as most observers expect - on August 30th, the Indonesian army will be left in control for up to four months before any international peacekeeping force arrives to supervise a handover of power.
It has also emerged that the United States opposed such a delay, but failed to secure agreement from Australia and Indonesia for the deployment of an armed international force immediately after the referendum. This was despite arguing that such a force was necessary to prevent pro-Indonesian militias plunging the former Portuguese colony into civil war.
Meanwhile, according to reports leaked to Australian newspapers, the UN has quietly prepared for a complete withdrawal of the current civilian UN presence of some 1,000 observers and unarmed police officers if civil war develops.
Many observers believe the post-referendum vacuum in East Timor will tempt integrationist forces to take the military initiative.
The Australian Foreign Affairs Minister, Mr Alexander Downer, will make the first visit by an Australian cabinet member to the territory today. He has denied a rift with the US over East Timor.
Some 430,000 voters have registered to choose between full independence or autonomy in the August 30th ballot.
However, the Sydney Morning Herald yesterday revealed that earlier this year the US Assistant Secretary of State for East Asian Affairs, Mr Stanley Roth, accused Australia of being "defeatist" for rejecting the idea of putting a multinational peacekeeping force on the ground immediately after the vote.
Without it, he told Dr Ashton Calvert, of Australia's Department of Foreign Affairs and Trade (according to the official report of their meeting in Washington), East Timor was "likely to collapse".
The Australian media are also reporting that the UN has drawn up secret plans for the eventual deployment of a peacekeeping force in East Timor - which would include the 2,800-strong Australian Army First Brigade stationed in Darwin.
But the UN had categorically decided that it would not send such a force into East Timor until after the Indonesian Parliament ratifies the referendum vote in November, when it meets to select a new president.
The US, Britain and Portugal would lend logistical support to such a body but were unlikely to provide troops, the Melbourne Age reported.
According to other documents leaked in Canberra this week, senior officers of the US Pacific Command were also pressing, as recently as June, for an international enforcement operation in East Timor after the vote.
Adding to Australian-US strains over how to handle the East Timor crisis, Mr Roth was rebuffed several times by Australia's ambassadors in Jakarta and Washington when he requested sensitive intelligence material on the links between the Indonesian armed forces and pro-Jakarta militias involved in a campaign of intimidation in the territory.
Australia said this departure from normal practice was to protect its intelligence sources on the ground.
However, the request indicated the depth of US concern over the potential of the Indonesian army to stir up violence after August 30th.
Events in Indonesia in recent days underline the dangers. On Monday and Tuesday this week, 22 people were killed by members of the army's strategic reserve command (Kostrad) in a Protestant church in Ambon, capital of Malaku Province (also known as the Spice Islands).
In the oil-rich Muslim province of Aceh at least 40 people were slaughtered by counterinsurgency forces on July 23rd. Amnesty International said that the Indonesian government's failure to address the human rights abuses of the past "sends a message to the security forces that they can continue to kill, disappear and torture people without being held to account".
Observers say the long delay between the June election in Indonesia and the selection of a new president has caused political drift in Jakarta, allowing the army, with its reputation for brutality, to take the lead as the situation deteriorates in restive provinces.
Complicating the picture further, the Indonesian armed forces commander, General Wiranto, has warned of serious unrest in Jakarta during November's parliament meeting, which will decide between President B.J. Habibie and popular opposition leader Megawati Sukharnoputri for president.
It is common knowledge that many generals believe East Timor must not be let go, so that it does not become an example to other separatist-minded regions.
In any post-referendum struggle in East Timor, elements of the Indonesian army are likely to arm and support the pro-Jakarta militias.
A secret Indonesian document leaked last month called on the Indonesian government to empower the pro-integration forces in the event of a vote for independence.
It was prepared by a special assistant to General Feisal Tandjung, co-ordinating minister for politics and security, and it instructed the pro-Jakarta paramilitaries to conduct a scorched-earth policy during any withdrawal to West Timor.
The future of East Timor, forcibly annexed by Indonesia after invasion in 1975, is, unlike Aceh, the subject of an international agreement forged earlier this year between Indonesia, Portugal and the UN.
Under the international spotlight, the security situation, while still serious, has improved in recent weeks.
Yesterday Indonesia replaced the commander in charge of East Timor, Col Tono Suratman. This may signal a change of tactics, as he has the reputation of being strongly promilitia.
In April, when the colonel met the Minister for Foreign Affairs, Mr Andrews, in the capital, Dili, he showed him crude home-made guns to try to persuade Mr Andrews that the pro-integration militias were making their own weapons and were not armed by the security forces.
On the same day he refused to take any action to stop militias slaughtering some 20 pro-independence supporters a few blocks away.
The military insisted the removal of Col Suratman was a regular rotation and not connected to the August 30th ballot on independence.
He was replaced by Col Muhamad Noer Muis in a short ceremony at military headquarters in Dili.
A senior Australian Foreign Ministry official told the parliament in Canberra yesterday that it appeared the Indonesian military was becoming less involved with East Timor's pro-Jakarta militias.
To head off trouble the UN is also preparing to set up a committee of 25 people on August 31st, representing both sides, to oversee the region during any political vacuum.
However, the US State Department spokesman, Mr James Rubin, on Thursday accused unidentified Indonesian officials of engaging in intimidation by suggesting a vote for independence would result in extensive violence, or even civil war.
What is certain is that the fate of the East Timorese, who have suffered repression at the hands of the Indonesian army for 24 years, will for several months continue to rest on Jakarta's armed forces in the aftermath of the vote, no matter how it goes.