Naylor Love builders working on an extension to the Countdown Dunedin Central supermarket, between Cumberland and Great King Sts, unearthed the lengths of matai, complete with steel adze marks.
The beams, believed to be more than 148 years old, were 2.64m below the surface of the supermarket car park.
The largest was 300mm by 400mm, and 4.64m long.
A just-released report written by Dr Jill Hamel for the New Zealand Historic Places Trust suggests the timber was most likely a "waterside structure" from a time when Dunedin's foreshore had still been largely unreclaimed.
"It was a little bulkhead.
"They called it a bulkhead.
"It's like just a little edging wharf that you can stand on and load something into a dinghy or a boat," Dr Hamel said.
She considered the presence of the structure showed Dunedin people made use of the lagoon in the days before the massive reclamation of harbour land.
"I was really startled to find there was a waterside structure in that lagoon."The lagoon occupied the space where, now, two city blocks stand - bounded by Moray Pl and Hanover, Great King and Cumberland Sts.
The site where the beams were found appeared to coincide with the edge of the entrance to the lagoon.
They had been covered by 300mm of black harbour silt.
Dr Hamel said it had been "frustrating", while trying to examine the site, to be restricted to a small 2m-wide hole rather than being able to expand the dig to a hole possibly as big as 20m by 20m.
"No way was Countdown going to pull up its car park to allow us to clear the timbers while they were actually in situ.
"It was like working down a keyhole."
Dr Hamel's report was paid for by Progressive Enterprises, the Australian owner of the Countdown Supermarket chain.
Dr Hamel believed it was quite possible the matai had been cut from one of the small pockets of native forest around the Otago Harbour.
The shape of the timber suggested that, before its use as a bulkhead, it could have been part of a ship builder's slipway for working on, and launching, small ships, or a "launchway" used to refloat stranded ships.
"The three largest [beams] were of the right dimensions to have been part of the cradle section of a slipway."
Some of the seven bolts found in the wood were more than 1m long.
Dr Hamel said the find had heightened her interest in what else might be buried around the edges of the former lagoon.
"Whenever any digging has to go on around where the edges of the lagoon is marked on the old maps, I think the trust [Historic Places Trust] will be showing extreme interest."
A Progressive Enterprises spokeswoman said the company was aware of the report but did not have any comment.
