The discovery has intrigued locals who are coming up with theories.
A Port Waikato business owner, who asked not to be named, said police had approached her yesterday looking for information. She had spoken to locals, many of whom believed the body could be that of a drug dealer from the Onewhero area who disappeared several years ago.
"This guy was a drug dealer and he went missing from here about eight years ago but he had a moon boot on his foot so I reckon it can't be him," she said.
Sunset Beach Surf Lifesaving Club president Malcolm Beattie believed someone had buried the remains on the sandhill years ago. Heavy tides and big swells had eroded a large section of the hill.
"I saw the area where the pathologists were working and they were working on a full skeleton - it wouldn't have washed in here," he said. "If someone is buried there's probably foul play involved somewhere along the line and obviously a person has suffered a bad fate."
Asked for his own theory about the remains, Mr Beattie could only think of a case "of about 10 to 12 years ago".
"There was this fellow who was an undesirable who was around the port a lot and was involved in the local dope scene and we didn't like him around the surf club," he said. "One weekend he was there and the next he was gone and people who knew him started to wonder where he was."
Counties Manukau police spokeswoman Ana-Mari Gates-Bowey said police estimate the skeleton could have been in its burial spot for five to 15 years.
She said police would search missing persons registers but they were of no use until they could verify how long the skeleton had been there. "Again, it's like looking for a needle in a haystack until we have some kind of time link to go on."
Ms Gates-Bowey said a guarded cordon was still in place but police canvassing the area were likely to wrap up their investigation today.
Anyone with any information is urged to call Counties Manukau Police immediately on (09) 261 1300 or Crimestoppers anonymously on 0800 555 111.