A New Zealand man in his 60s is the owner of the boat raided with a substantial amount of cocaine onboard.
In total New Zealand and Australian authorities seized 1.4 tonnes of cocaine valued at more than $300 million.
It marked the end of a joint two-and-a-half year investigation into an alleged drug network involving New Zealand authorities and the Australian Federal Police.
Six people have been arrested, including the New Zealander, with more expected.
The yacht was intercepted off the New South Wales coast last week where the "significant" amount of the Class A drug was seized.
Australian authorities said a transnational drug syndicate had used the yacht to sail to a "mother ship" waiting in international waters before federal police officers pulled off the largest cocaine bust in Australia's history.
Australian Federal Police say the record haul of 1.4 tonnes of cocaine - worth more than $312 million - was seized from the yacht Elakha off the NSW south coast on Thursday night.
New Zealand customs had been tracking the Elakha for four years and shared intelligence with their Australian counterparts in an "Anzac-spirited" operation.
The yacht travelled from New Zealand to the "mother ship" in the south Pacific Ocean and was then intercepted 370km off the coast, AFP Acting Deputy Commissioner Neil Gaughan said on Monday.
A 63-year-old New Zealand man and a 54-year-old dual national of Swiss-Fijian origin were on board with the massive drug stash, authorities say.
The following morning four other men - a 66-year-old, two 62-year-olds and a 32-year-old - were also arrested in Sydney and on the south coast.
They're accused of planning to meet the yacht and bring the drugs ashore in NSW.
The men face maximum sentences of life imprisonment.
"This syndicate was intending to bring significant misery to the Australian community," Mr Gaughan said in Sydney.
"Any organised crime syndicate that believes they're going to get away with it, sooner or later they're going to get caught. You take the risk."
Police also seized large quantities of cash, jewellery and electronic devices and expect to make more arrests.
Mr Gaughan said the mother ship remained under investigation. Elakha's owner is among those facing charges.
Three of the men were due to face Sydney's Central Local Court on Monday while the three others will appear on Wednesday.
The Elakha remains at a Border Force facility in Sydney's Neutral Bay.
Federal Justice Minister Michael Keenan expects the bust to drive up the street price of cocaine in Australia - which was already relatively high.
"Clearly this is an enormous blow to supply of illicit drugs in Australia, particularly cocaine," Mr Keenan told reporters.
Police say the men had known each other for decades and there was a connection with a New Zealand group.
Newshub / NZN