Hamish McDonald – Indonesian submarines and combat aircraft shadowed so closely ships carrying Australian and New Zealand troops into East Timor in 1999 that escorting warships went onto full battle stations alert, it has been revealed.

The "aggressive probing tactics" by Indonesian aircraft against the Australian-led intervention force, Interfet, led to Australia placing F/A-18 fighters on readiness to patrol over Timor and having F-111 strike aircraft "bombed up" to knock out Indonesian communications as far back as Jakarta.

Revelations about the tensions caused by Indonesian deployments of submarines, missile-boats and fighters during the first two weeks of the operation cast a new light on the approach by Interfet's commander, the then Major-General Peter Cosgrove.

They should help dispel lingering resentment in Indonesian military and political circles that Interfet took an unnecessarily "aggressive" and "arrogant" posture during the transfer of control in East Timor.

Many details of the Indonesian manoeuvres are made public for the first time in the forthcoming issue of the journal Contemporary Southeast Asia, by the New Zealand defence expert Dr David Dickens, director of the Centre for Strategic Studies in Wellington.

His article cites highly placed Australian and New Zealand defence sources, and the Herald has independently confirmed some aspects of his account, including submarine movements.

Dr Dickens argues that despite the co-operation General Cosgrove received from the army and police when he landed in Dili, the naval and air threats meant "a show of overwhelming force was still necessary".

The Interfet force, which set off for Dili on September 19, 1999, initially comprised about 5,000 troops, mostly from Australia and New Zealand. It was transferred and protected by ships from Australia, New Zealand, Britain, France and the United States.

General Cosgrove flew into Dili ahead of his troops without a personal bodyguard or weapons, determined to strike a co-operative relationship with the Indonesian ground commander, Major-General Kiki Syanakri.

Indonesian forces in East Timor were about 15,000, outnumbering the Interfet force by three-to-one. When the forces arrived by air and sea the next day, General Cosgrove succeeded in making it seem like a routine exercise, despite the Indonesian-directed operation to raze the territory's buildings and infrastructure and deport its population.

At the same time, he aimed to show determination by bringing in his forces quickly, and immediately beginning security operations in Dili. "The shock generated by this force, professional and well-equipped, and deployed with speed, made it appear larger than it was when deployed," Dr Dickens notes. Behind the scenes, the Australian Defence Force made contingency plans in case the Indonesian military, the TNI, decided to contest the landing. The Indonesian Navy's two German-built Type 209 submarines appeared around East Timor and the air force deployed aircraft, including a small number of fighters, to West Timor, from where they adopted "aggressive probing tactics". "These tactics raised questions about the intentions of the TNI," Dr Dickens writes. "Various Interfet ships went to action stations during these incidents."

The submarines shadowed the Interfet fleet, with one of them detected by the frigate HMNZS Canterbury close to the landing of New Zealand soldiers at Suai. The submarine contacts were passed on to defence headquarters in Canberra, which took them up with Jakarta. "In response, and once the Australian higher level commanders had provided information on the location of the submarines that was convincing, the appropriate TNI commander admitted his submarines had been deployed and agreed to retire them from the area," the article said.

The air threats were tracked by the cruiser USS Mobile Bay, while the RAAF put combat units in northern Australia on a "very high" state of readiness. As well as preparing the F/A-18s of the RAAF's No 75 Squadron and New Zealand's Skyhawk fighters at Tindal air base to provide air cover and ground strikes, contingency plans included higher level threats.

Dr Dickens was told by defence sources, although he has not included this in his article, that the alert also involved the F-111 strike aircraft at Amberley air base, near Brisbane, which were "bombed up" and ready to knock out communications as far back as TNI headquarters on the outskirts of Jakarta if necessary.

The pattern of aggressive movements by Indonesian submarines, missile craft and fighters tapered off within two weeks. By September 28 the TNI had only 1,200 troops in East Timor. With the threat ebbing and Interfet gaining control outside Dili, the RAAF took its squadrons to a lower level of readiness, and several warships were withdrawn.