Harbourmaster Heath Cairns said the two people had been safely recovered by the harbourmaster team, however the sunken vessel was still underwater.
He said with the current lake conditions they could not salvage the boat today.
The plan was to retrieve it on the next calm day, he said.
Senior constable Barry Shepherd of the Taupō police said a man and a woman had been rescued from rocks on the shore of Lake Taupō after their boat sank.
He said the rocks were on the western side of the lake near Kinloch.
"Another person rang police after seeing them. the Lake Taupō Coastguard and harbour master responded and rescued them off the rocks."
Shepherd said the conditions on the lake were windy but he was unsure if the conditions had contributed to the boat sinking.
"It could be any one reason or a combination of reasons."