Some of the eight bludgeoned pups were just days old, said Conservation Minister Kate Wilkinson. She appealed for assistance from the public to help track down the attackers.
"To go around and club 23 seals to death over a number of days is very deliberate and you have to question the state of mind of someone who can carry out such a cruel and abhorrent attack," Wilkinson said in a statement.
The Ohau Point seal colony on northern South Island is a popular tourism spot north of the town of Kaikoura, which is an international whale-watching center.
The Department of Conservation said the attacks took place over as long as two weeks. The location may have delayed the discovery.
The colony stretches about 1.2 miles along the coast and is at the bottom of a steep, 100-foot cliff with no easy access, department spokesman Rory Newsam said.
Fur seal numbers are gradually increasing in New Zealand after the species was nearly exterminated by hunters in the 1800s. The midsize seals are not native to New Zealand.
The Ohau Point colony was only reoccupied for breeding in 1990, and about 600 fur seal pups were born there in 2004, said Bruce Robertson, a seal specialist and senior lecturer in zoology at Otago University.
He said the long-term losses for the population could be dire. The attacks killed 13 breeding females, which meant 13 pups dependent on their milk would die and fewer pups will be born next year, Robertson said.
"Given this colony is increasing in size, this loss of life is a small setback," he said Monday. "However, large mammal populations cannot sustain the repeated loss of breeding females [and] any external influences can be detrimental."
Other live seals at the colony had been seen with injuries for the attacks, Department of Conservation area manager Dave Hayes said. The weapon used was a bat or club, he said.
Under New Zealand law, killing or harming fur seals or other marine mammals incurs up to six months in prison or a fine of up to 250,000 New Zealand dollars (US$191,000).
A further fine of up to $7,600 for each marine mammal killed or harmed can also be imposed by the court.