The I-124 warship has been resting in its watery grave off Darwin's coast since it was sunk by the HMAS Deloraine on January 20,1942.

The submarine had been part of a squadron waging covert operations against Australia's north, laying mines and attacking ships in waters near Darwin.

An unsuccessful attack on a US convoy in the region by a sister submarine prompted the Royal Australian Navy to send ships to investigate. The I-124 fired a torpedo at the first ship to arrive, the HMAS Deloraine, which in turn detonated dozens of depth charges in a sustained attack that sank the Japanese warship. The 80 submariners remain on board.

A historic scientific expedition to the wreck last November provided new insight into one of the most significant places of shared history between Australia and Japan.

While previous surveys had utilised remote sensors to develop models of the submarine, this was the first-ever authorised scientific dive down to the wreck, which rests on the seabed between Darwin and Bathurst Island.

A team of specialist archaeologists and divers descended over 50 metres to the site to gather baseline data and capture vision of the first wreck in Australia to be protected under Commonwealth legislation.

The images were used to produce a 3D model of the I-124, which established a clear picture of the condition of the wreck that will assist with future site management and conservation.

Minister for Arts, Culture and Heritage Chansey Paech, said the I-124 was one of the Territory's "fascinating war stories" and one of the most significant wartime wrecks in Australian waters.

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"The recent expedition was critical to understanding this chapter in the defence of Australia during WWII," Mr Paech said.

"The findings provide insight into the design of the submarine, and the historic engagement with Allied forces that led to its sinking. "Understanding the wreck at this level of detail and accuracy will be invaluable in managing it into the future."

The voyage is the subject of a short documentary which reveals the findings, and tells the story of those who inspired and carried out the expedition which has been supported by the Australian and Northern Territory Governments, Paspaley Pearls, Major Projects Foundation, Flinders University, and the Australian Japanese Association of the NT.

"This documentary highlights the importance of nations working collaboratively to protect fragile and significant places of shared heritage," Mr Paech said.

"It is a behind-the-scenes glimpse into the historic voyage down to the wreck and is an interesting addendum to the fascinating story that began in Japan and ended in Darwin's deep seas."