Speaking to journalists, Deputy Foreign Affairs Minister Francois Wu agreed the proposal floated by Japanese Prime Minister Shigeru Ishiba for a NATO-like security pact in Asia would likely anger Beijing.
"Maybe it's not good for the stability of the region," Mr Wu he told a group of Australian reporters at the Ministry of Foreign Affairs in the capital Taipei in November.
"But having said that ... AUKUS in some way, is another form of (an) Asian NATO."
The North Atlantic Treaty Organisation is an alliance of 30 European and two North American nations set up to defend each other against attacks by third parties.
"You just don't need to call (AUKUS) NATO, but it is a real NATO," Mr Wu said.
Under the AUKUS partnership, Australia has been promised at least three Virginia-class submarines from the US in the early 2030s, with a new class of nuclear-powered boats to be built for delivery from the 2040s.
Under AUKUS, Australia will buy several Virginia Class subs, like the USS North Carolina (pictured). (Aaron Bunch/AAP PHOTOS)
In a joint statement, Australia, the UK and US earlier this year said they were consulting with New Zealand, Canada and South Korea to identify possibilities for collaboration on capabilities under AUKUS Pillar II, which covers advanced capabilities.
Beijing has warned New Zealand if it were to join the partnership, it would inevitably have a negative impact on the country's relationship with China.
Mr Wu said while Taiwan couldn't join these agreements because of Beijing's opposition, it would be good for countries such as Japan, Canada or New Zealand to do so.
US president-elect Donald Trump has made comments about Taiwan, saying it should pay the US for its defence, prompting concern amongst officials about how Washington's position may change after his inauguration in January.
Mr Wu questioned how Mr Trump could make the US "great again" if he abandoned Taiwan.
"He will lose the credibility of the US in the total Asia-Pacific," he said.
"Every day we need to send a message to (Chinese President) Xi Jinping, not to invade Taiwan."
It's not clear how the US stance on AUKUS, and Taiwan, will change under the new administration. (Pat Hoelscher/AAP PHOTOS)
Australian National University expert associate Jennifer Parker said while AUKUS was not a de-facto NATO, and was a capability rather than a security pact, it had been positive to see its increased acceptance in the region.
"Different regions require different security constructs - And the NATO-like structure that relies on an aligned strategic outlook is not likely to be a successful model for Asia - as evidenced by the failure of the (1954 Southeast Asia Treaty Organisation, which was dissolved in 1977)," she told AAP.
"We are a long way off from additional countries joining Pillar II of AUKUS, if ever.
"But we will certainly see increased  collaboration on AUKUS initiatives under Pillar II with countries such as Japan, Canada, New Zealand and South Korea."
A senior Taiwanese official speaking anonymously said the island welcomed the passage of Australian warships through the strait, and would like to see more of it.
Warships from Japan, Australia and New Zealand sailed through the Taiwan Strait in late September, prompting Beijing to warn it remained vigilant against any acts that might jeopardise its sovereignty.
Ms Parker said transits through the strait by European and regional navies alongside Australia's, had increased in the last 12 months.
"They are an important method of highlighting that the Taiwan Strait is international waters and reinforcing support for the UN Convention on the Law of the Sea in the face of China's regional attempts to challenge these norms," she said.
China claims self-governed Taiwan as a breakaway province after the government of the Republic of China (Taiwan) relocated to the island in 1949 during the civil war with the Chinese Communist Party.
The AAP reporter travelled to Taipei with the assistance of the Taiwanese government.
