The man will appear in Rotorua District Court on Monday.
Police are not seeking anyone else in relation to the incident.
A scene examination is being carried out and detectives are making several enquiries as well as providing support to the victim's family.
A nearby neighbour earlier said there had been no indication anything was wrong and the first she knew was when she noticed a lot of police gathering at the property at around 10am. She did not see an ambulance.
The property has been cordoned off, along with half the adjoining property.
Police could be seen working on the deck at the front of the house, which was shielded by a green tarpaulin. Security was in place at the cordon.
Five Mile Bay is a small settlement of mainly holiday homes about 8km south of Taupo.