Police say the man launched from the Tasman District on Monday morning, attempting to cross the Cook Strait.
However, he failed to arrive at his destination on Plimmerton Beach.
A search and rescue operation began on Tuesday morning with police vessel Lady Elizabeth IV, Marlborough Search and Rescue and Bluebridge Rescue currently in the Cook Strait, north of the Queen Charlotte Sound.
"Police and SAR teams have been conducting a water search with the assistance of Coastguard and RCCNZ," a police spokesperson said.
A jetski was located near Cooks Rock in the Cook Strait yesterday evening, the spokesperson said.
It was believed to be the one belonging to the missing man.