The wreck of a launch was found off Wedge Point in Picton Harbour

A mystery wreck has been discovered at the bottom of Picton Harbour during a Defence Force training exercise.

Navy hydrographer lieutenant Robin Kuhn said the wreck was discovered by a team searching the harbour's seabed for navigational obstructions.

The yacht, which was about 9.8 metres long and 4m wide, was discovered on Friday about 400m east of Wedge Point.

It was at a depth of 36m, Kuhn said.

"We spoke to the [Marlborough] harbourmaster and some of the locals and no-one seems to know what it was."

"It's a little bit of a mystery ... it's not charted and no-one seems to know about it."

The discovery was made using an underwater robot following a pre-programmed route, moving backwards and forwards to scan sections of the seafloor.

"It's almost the same as mowing the lawn," Kuhn said.

The data collected by the robot was then downloaded onto a computer.

The yacht did not pose a danger for boats passing through the area, Kuhn said.

As well as the yacht, a large concrete block was discovered in the middle of the harbour

"Other than that Picton Harbour was reasonably clear of objects."

Spotting the wreck was a surprise for the team, Kuhn said.

"We were searching for other objects under the water and weren't expecting to see a yacht."

"It was quite cool to see the image come up so clearly. It's nice to see it because it shows the system's working and is able to pick up on things like that."

Marlborough Harbourmaster Alex van Wijngaarden said he was in discussions with the Navy about the discovery, but would not comment further.

The exercise to survey the Picton Harbour seabed was part of Exercise Southern Katipo, a joint operation involving more than 2000 naval, army and airforce personnel.