A scene guard was in place at the property overnight and a scene examination will continue today.
"Police can confirm that this incident took place on Seaforth Rd, near a property where a man was killed on 1 January," said Detective Sergeant Andrew Saunders.
"There is nothing to suggest at this stage that there is any connection between the two deaths.
"We understand that these two incidents will have been very unsettling for Waihi Beach residents.
"We want to reiterate that these incidents involved people known to each other, and there is no risk to the wider community."
Investigators were on the scene for most of Sunday where the alleged murder took place. Photo / George Novak
Waihi Beach residents can expect to see an increased police presence in the coming days as reassurance patrols are carried out.
"Except for the fact that both families have lost someone. It is absolutely horrendous for them."
Resident Bill Hedges just moved to Waihī Beach before Christmas.
"The whole reason we bought here was the peaceful, quiet, close community."
He didn't wake to sirens last night and hearing about the second death this morning was "quite a bit of a shock".
"Nobody wants to be in a place where you have one homicide investigation, now we have two."
Mayor View Volunteer Fire Brigade chief fire officer Peter Harwood said members were called out to the Seaforth Rd death on New Year's Day but not last night.
