The Police Maritime Unit, Coastguard and a rescue helicopter were also assisting with the search effort.
Police urged people to avoid or delay unnecessary outdoor activities around Wellington due to the severe weather conditions.
"Conditions are dangerous on the water and on the roads due to high winds, and we urge people to take precautions and keep safe."
Speaking to the Herald at Owhiro Bay, Wellington mayor Andy Foster said he was baffled by the kayakers' behaviour.
"It's the sort of thing where you go 'what on earth were you thinking'," he said.
"It's absolutely nuts being out in those kinds of weather conditions.
"There's obviously some very proficient kayakers but you're putting yourself at risk and you're also putting other people at risk. It's not responsible behaviour.
"Stay off the water is the message … being out on the water, that's not a good idea."
He said the conditions had so far been better than expected, with no debris reported on the roads or affecting houses.
Their main concern was for tonight, he said, with predictions for a higher wave height at the next high tide.
"The advice is still there at the moment which is batten down the hatches, keep pets inside and anything that's likely to blow away.
"And just be prepared with the grab bag if you're one of those properties that have been affected before, just in case you need to evacuate."
