The seal, believed to be an adult fur or leopard seal, disappeared into the sea after the attack.
While there have been a number of seal sightings around the country lately none have resulted in an attack.
Department of Conservation staff from Wairoa were called and have been checking to see whether the seal has come ashore again.
The boy's wounds were treated in hospital this afternoon.
Department of Conservation East Coast conservation services manager John Lucas said the most likely scenario was that the boys were jumping from rock to rock which startled the seal.
"When wild animals are threatened they will go into flight or fight mode. This seal chose to fight," Mr Lucas said.
"At this time of the year seals tend to spend a lot of time around our shore particularly after bad weather."
He said with more chance of interaction people need to treat seals like wild animals and not approach.
"People need to be vigilant and aware that the seals can react," Mr Lucas said.