Plank by plank, one of Australia's most effective World War II secret weapons is being restored to its original wartime condition to serve as a memorial for the conflict's most elite commandos.

MV Krait was a humble Japanese fishing vessel that enabled its crew to slip under the radar and sink more enemy shipping than any other vessel in the Australian Navy during the war.

Sorry, this video has expired The men of Operation Jaywick disguised themselves as Malay fishermen aboard MV Krait to enter enemy territory undetected.

MV Krait ferried 14 commandos, disguised as Malay fishermen, thousands of kilometres behind enemy lines into Singapore Harbour as part of Operation Jaywick in 1943.

The mission? To blow up enemy shipping in the heart of Japan's wartime stronghold. And it worked. The men returned home to Australia undetected, leaving the Japanese command reeling.

The men involved in this extraordinary raid became part of the top secret, so-called Z Special Unit.

Their heroism was unacknowledged during the war, and members of the unit were sworn to secrecy even after the conflict ended.

MV Krait is owned by the Australian War Memorial, but is on loan to the Maritime Museum. ( Supplied: Quentin Jones )

MV Krait was returned to Australia in 1964, with a huge event around Sydney Harbour. ( ABC News )

Since the Australian War Memorial acquired the boat in 1987, the 20-metre-long vessel has rocked with the tides at the Australian National Maritime Museum in Sydney's Darling Harbour.

Z Special veteran Douglas Herps, who undertook missions behind the lines in Borneo, was worried the wooden vessel would deteriorate if it remained in the water and history would be lost.

He spent the last few years of his life campaigning for MV Krait to be preserved out of the water, as a memorial to all of those who served in Australia's Special Operations teams.

Before his death in April 2015, at age 91, Mr Herps convinced both the Australian War Memorial and the Australian National Maritime Museum to house MV Krait on land, in a major expansion to the museum.

New teak planks are replacing some damaged sections of MV Krait. ( Australian Story: Winsome Denyer )

Two years after his death, the first step of Mr Herps' dream is underway, with MV Krait now undergoing essential restoration work.

A $500,000 grant from the Australian Army helped kickstart the project. The Australian War Memorial, the Australian National Maritime Museum and the Herps family also made contributions.

But like any historic restoration project, there have been a few unexpected "surprises".

Douglas Herps served as part of the Z Special Unit. ( Supplied/NewsCorp: Rohan Kelly )

"When we stripped the planking off, we saw exactly the extent of the damage. We found that the framing itself needed work also," hull surveyor Warwick Thomson said.

"You've got to remember this is an 83-year-old vessel and she needs a lot of TLC to get her back into a structural and water-tight integrity condition."

Mr Thomson and the team of young shipwrights at Michael Bartley Shipwrights have 12 months to restore the boat's hull using new teak planking, replace the decks, and then convert the layout back to the configuration at the time of Operation Jaywick.

The cost of restoring MV Krait has blown out after more damage was discovered. ( Australian Story: Winsome Denyer )

Unfortunately, the extensive damage means there is currently not enough money to complete the restoration.

Mr Herps' family and friends are continuing to campaign for funds to ensure the MV Krait project is finished.

In the meantime, everything of historical significance is being saved, including the original nails and planks of wood removed from the boat, to be used in museum displays.

The original nails from MV Krait will be kept as part of the memorial display. ( Australian Story: Winsome Denyer )

Retired Major General Brian Dawson from the Australian War Memorial said the MV Krait display would help acknowledge the men who served in secret missions.

"The Krait is really a symbol of what these men did, but not just them, those who followed in the latter part of the Second World War," he said.

Plans have been drawn up to extend the Australian National Maritime Museum to eventually house MV Krait, but that will require millions more in funding to make it a reality.