Mr Duncan (46) had been missing since last Sunday morning, having last been seen on his cabin boat, Sundance II, setting out from an area near the TSS Earnslaw slipway about 9.30am.
The boat travelled several hundred metres and then stopped in the middle of the lake.
It then either drifted or made its way towards the shore and the Bay View Rd boat ramp, at Kelvin Heights, about an hour later.
However, late Sunday afternoon the boat was found to be empty.
Aerial and land searches failed to locate Mr Duncan, the owner of Painting Solutions, so the Police National Dive Squad was called in to assist on Tuesday morning.
They were supported by Royal New Zealand Navy staff, who had used advanced sonar equipment to comb the bottom of the lake, which was between 30m and 33m deep in the search area.
Mr Duncan's death will be referred to the coroner.
