A Te Awamutu farmer is believed to have had a tragic accident after his boat was found empty off the Tauranga coast on Tuesday.

The missing man is Carl Earwaker, 39.

His fibreglass Sea Nymph, named Optimist, was found two nautical miles south of Mayor Island on Tuesday.

Tauranga police were initially unsure if it had been occupied. An extensive sea and air search by police, Coastguard, private vessels and aircraft was unsuccessful, a police spokesperson said.

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"Police believe Mr Earwaker has had a tragic accident and for reasons not yet fully known the boat has capsized.

"A surface search of the area where the boat was located is continuing today by police and Mr Earwaker's family.

"Police's thoughts are with Mr Earwaker's family and friends."

This afternoon the police dive squad and Navy will begin a seafloor search in the same area.