Detective Senior Sergeant Greg Turner of Tauranga Police said the man had been on board the boat by himself. His death would be referred to the coroner.
Police were seen on board a Coastguard vessel inside a restricted area late on Saturday afternoon. Tied to the Coastguard vessel was a white 8.8m sailboat.
Turner said members of the public found a yacht with no one on board and a body was found in the water soon after.
"The Coastguard arrived soon after they were notified and pulled the man from the water but he was not able to be revived."
The drowning was the second on Friday afternoon - St John Ambulance crews and police rushed to Maori Bay west of Auckland shortly after 3.30pm on Friday where a 21-year-old man had died.
Police have named the man as Akhil Tangri. He was an Indian national had only been in New Zealand for a number of months, police said in a statement.
Officers spoke to witnesses and provided support to the man's friends.
The weekend, which was the first official weekend of summer, was also a busy weekend for lifeguards working to keep people safe on the water.
Lifeguards up and down our coastlines carried out 11 rescues, 11 "assists" or preventative actions and three major first aids.
No one had to be plucked from our waters by surf life saving officials over the same period last year.
Sunset and Kariotahi Lifeguards were kept busy on Sunday responding to a vessel that was overdue on Waikato Bar, but the vessel was later confirmed to be safe and well.
