About 1.4 tonnes of the drug were found on a New Zealand yacht, the Elakha, when it was intercepted about 370 kilometres off the NSW South Coast in the early hours of Friday, police said.

Police allege the Elakha had travelled from New Zealand and met a "mother ship" in the South Pacific Ocean last month to collect the drugs.

The cocaine was intended to be transferred from the Elakha to a motor boat that was due to leave from the small NSW South Coast town of St Georges Basin.

However, three men - David Wren, 66, Kevin Michael Geraghty, 63, and Glen James Willcox, 62 - were arrested in St Georges Basin on Friday before they could head out to sea.

They were arrested hours after naval officers from HMAS Bathurst intercepted and boarded the Elakha and found several black bags containing blocks of cocaine.

The massive haul has an estimated street value of $312 million.

Two crew members, New Zealand man Hamish Thompson, 63, and dual Swiss-Fijian national Valentino Fries, 54, were arrested aboard the Elakha.

The yacht was towed back to the Australian Border Force base at Neutral Bay on Sunday.

The sixth man, Yahay Magdalawi, 32, was arrested in Sydney on Friday.

The men have known each other for decades, Australian Federal Police acting Deputy Commissioner Neil Gaughan said.

They have all been charged with conspiracy to import a border-controlled drug, a charge that carries a maximum life sentence.

Police also seized large quantities of cash, jewellery and electronic devices and expect to make more arrests.

Mr Thompson appeared in Central Local Court via video-link from Surry Hills police station on Monday, barefoot and wearing cargo shorts and a T-shirt.

Mr Fries appeared in jeans and a printed shirt with a grey beard.

Legal Aid lawyer Deone Provera did not apply for bail for the men and they will re-appear in court on Wednesday along with their four co-accused.

The operation was the culmination of a two-year investigation by federal police and Australian Border Force as well as authorities from New Zealand, Fiji and French Polynesia.

However, it started with a tip-off from New Zealand authorities, who had been watching the Elakha for more than four years.

"No one gets to see the blood, sweat and tears that go into this type of investigation," Mr Gaughan said.

"The interception of this huge volume of drugs and the charging of these six men is a testament to the officers' drive and determination."

Minister for Justice, Michael Keenan, said the intercept would put a significant dent in the supply of cocaine along the east coast of Australia and would drive up prices.

Several major cocaine busts over the past few months are proof that Australia is a "honey pot" for organised criminal drug syndicates.

One kilogram of cocaine sells for $26,000 in America but in Australia it sells for $240,000 due to the higher street price.

In America, a gram of cocaine costs a user $50-$100 whereas it starts at $300 in Australia.

"You can see why this acts as a honey pot effect for organised criminals around the world," Mr Keenan said.