Last night, police charged two men with the theft of the boat.
The men, aged 22 and 25, will appear in Tauranga District Court tomorrow.
Police were still trying to find the other man who was in the boat at the time of the capsize, Liam Kane, 22.
He has not been seen since raising the alarm with a member of the public on Tuesday night.
Police said none of the men were experienced on the water and the weather conditions were poor.
The aluminium dinghy was discovered at Matakana Island yesterday morning by members of the Mt Maunganui Surf Club, as they searched the waterways in an inflatable rescue boat.
The dinghy was upside-down near the base of cliffs between Matakana Point and Tahunamanu Point, directly north of Omokoroa Point, where the men set off from.
It appeared to have been pushed towards Matakana Island by the wind and current.