An Indonesian Cakra-class submarine (KRI Cakra or KRI Nanggala (tragically sunk alone in 2021) was involved in the following confrontation with Australian and New Zealand warships in 1999. Source: the operational history of Indonesia’s 2 Cakra class submarines - 1999 East Timor (ET) Crisis.
GEO POLITICAL BACKGROUND
Tiny ET (see map below) a former Portuguese colony, was brutally invaded by Indonesia in 1975. ET is less than 700km from Australia and borders Indonesian West Timor.
By early 1999 UN, US and Australian political pressure forced Indonesia to accept an an August 30, 1999 Referendum in which ET voters overwhelming favoured rapid independence from Indonesia.
After the Referendum, rightwing, moderately Muslim, military officers who (under the surface) still dominate Indonesia were outraged ET was to secede from Indonesia. In contrast ET was and remains a Catholic Latin leftwing country. Indonesia was concerned other islands of the difficult to control Indonesia Archipelago (like almost majority Christian West Papua/West Irian) would be encouraged by ET's success.
Immediately after the August 30, 1999, Referendum Indonesian rightwing military leaders launched a "militia" (thugs paid by the Indonesian military) offensive to crush East Timorese independence. The UN, US and Australia objected to this new Indonesian militar action.
By late 1999 relations between Indonesia and its southern neighbour, Australia, were extreme.
INDONESIAN NEAR TORPEDOING OF AUS/NZ SHIPS
As Australia was the closest democratic military power trusted by the UN-US, Australia rapidly led an air and sea liberation of ET in late 1999. Naturally this led to some confrontations with Indonesia naval and army and active INTERFET suppression of Indonesia Army paid militia forces in/around ET.
Royal Australian Navy (RAN) transport vessel, HMAS Kanimbla, was to serve as an INTERFET command post.
As HMAS Kanimbla approached the coast of East Timor, it entered what were technically still Indonesian waters. One of the two Indonesian Cakra-class submarines (KRI Cakra or KRI Nanggal) was conducting routine patrol duties in the Timor Sea, when the Cakra-class sub's sonar detected several unidentified surface ships moving towards Dili.
The Cakra-class submarine commander ordered his sub to submerge to periscope depth for potential action. The unidentified surface ships turned out to be HMAS Kanimbla and two Royal New Zealand Navy (RNZN) frigates. The submarine captain ordered preparations for firing torpedoes.[3] The New Zealand frigates were aware of the presence of the submarine and could have eventually sunk it with their own lightweight anti-submarine torpedoes, but initially they were unable to determine the sub's exact position.
At that point, the commander of HMAS Kanimbla communicated with the Australian government regarding the situation. The Australian government (in Canberra) emergency contacted the Indonesian government (in Jakarta) requesting permission for the INTERFET vessels to enter Indonesian waters to continue passage to Dili, capital of East Timor.[3]
Fortunately naval headquarters in Jakarta ordered the submarine not to obstruct/torpedo the convoy. This averted the open warfare between Australia and Indonesia that submarine torpedo damage or sinking of an Australian or New Zealand ship (and Aus NZ retaliation) would have triggered. The submarine then surfaced (to show non-aggressive goodwill) but continued to shadow the convoy for the rest of the convoy's passage to Dili.[3]