An old Navy boat that ferried World War II forces behind enemy lines has finally been pulled out of Darwin Harbour, after several failed attempts.

MV Rushcutter, known as HDML 1321 during the war, was used by Australia's Z Special Unit to transport commandos to covert operations in Papua New Guinea.

The boat sank in the harbour almost two years ago and the Darwin Port then pulled it to a safer position near the Catalina boat ramp at East Arm.

A small group of volunteers known as Save Motor Launch 1321 purchased the boat from its former private owner for $2 and has been trying to recover it ever since.

"We did it," the group's chairman Robert Welfare said.

"Lots of pumps, lots of volunteers, lots of time, lots of planning."

A diver prepares to enter the water at Darwin Harbour. ( ABC News: Felicity James )

Mr Welfare said he shed a tear when the boat floated into its position above a submerged trailer, with the help of several water pumps and a volunteer diver early on Sunday morning.

"Oh a little one, it could've been spray off the pumps," he said.

"It was just wonderful that we got it right on the third attempt."

A small group of volunteers bought the vessel for $2. ( ABC News: Felicity James )

Mr Welfare is a lawyer who also has marine qualifications and said many of the volunteers were also lawyers who are keen to get out of the office.

"All these chaps that are surrounding me, it shows what can be done if everyone pulls together, pulls on the same oar."

The ABC understands the Northern Territory Government put about $120,000 towards a purpose-built trailer to cradle the boat out of the harbour.

Other businesses have donated machinery and funds.

Mr Welfare said he shed a tear when the boat floated into position. ( ABC News: Felicity James )

The Darwin Port has extended several deadlines for the boat's removal from the harbour, initially issued to its former owner Tracy Geddes.

Save Motor Launch 1321 bought the boat from Ms Geddes when she ran out of funds for its restoration and failed to sell it before it sank in 2016.

"We just couldn't afford it anymore and we advertised it, and that's a story in itself," she said.

Volunteers inspect the MV Rushcutter after floating it onto its trailer. ( ABC News: Felicity James )

There wasn't much interest from potential buyers apart from one man who Ms Geddes said turned out to be "of interest" to police and did not complete the purchase.

Mr Welfare said the group's plan now is to restore the boat and eventually get it back in the water.

According to the Darwin Military Museum, eight commandos used the boat in 1945 to go behind enemy lines in Papua New Guinea as part of Operation Copper.

The harbourmaster watched on as the rescue mission got underway. ( ABC News: Felicity James )

Seven of those commandos lost their lives and one survived.

"It's a very historic object," Mr Welfare said.

"Many people lost their lives on this boat, it saved people off beaches, it took Americans off beaches, it took Australians off beaches."

"It contributed significantly to the [World War II] effort on the islands north of us here."

A crane helped pull the MV Rushcutter from the water on Sunday afternoon after the successful float.

Mr Welfare said the boat would then be driven to a landing barge, which would ferry it to an undisclosed location.