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The deceased were a 49-year-old woman and a 50-year-old man, both from the Bay of Plenty.
"We're not in a position to release the names at this stage," a police spokesman said.
Emergency services were alerted to the bodies at about 7am on Friday, near Mere Rd in Taupō.
Detective Senior Sergeant Ryan Yardley said then police were making inquiries after the two bodies were found by a member of the public just after 7am.
"At this stage, police are working to establish the identities of the bodies, and a post mortem examination will be conducted," he said.
A scene guard was to remain in place.
Taupō Mayor David Trewavas said he understood a person out walking along the lake saw the bodies in the water.
The bodies had then been pulled in from the shallows, he said.
"This is a very, very sad day," Trewavas said.
He understood there had been no sign of a boat near where the bodies were found which added to the mystery of how the pair came to die.
Taupō had been particularly busy in the past week, as people poured into the popular central North Island holiday destination from across the country.
Trewavas said learning two people had perished overnight in his town was a tragic way to start the day.
"To wake up on a beautiful crystal-clear day, the lake is so pristine and for someone to come across two people dead is very, very unfortunate."
The Lake Taupō Coastguard said it had not been contacted about the deaths, nor had there been any search on the lake for missing boaties.