Last night's search involved five boats, including the Wellington Coastguard, the Westpac Rescue helicopter, Land Search and Rescue volunteers scouring the shoreline, until it was called off about 2am.
The man's yellow kayak was found last night on the shore about 6km from Ward Island in the Pencarrow area. A rucksack and paddle were also found, in the water.
Hamilton police Senior Sergeant Craig Taylor said the man's family were understandably still in shock.