The East by West ferry City Cat was also in the news in October 2015 when it came to the rescue of three kayakers in distress. (File video)

A capsized kayaker in freezing water forced the East by West ferry to divert for an emergency rescue operation.

The ferry, which traverses Wellington harbour, changed its route on Monday afternoon to save a trio of kayakers who got into trouble about 200m offshore from Matiu-Somes island.

Maritime police said the ferry picked up the kayakers and dropped them at the island after one fell out of his boat.

SUPPLIED One kayaker had fallen out of the boat and could not get back in.

After he fell out, he was unable to get back in, witnesses said.

The man was gripping onto the back of a friend's kayak as a cold wind whipped up choppy seas around them.

Another kayaker, who had lost his paddle, attempted to get himself to Matiu-Somes using just his hands.

Seeing the flailing watersportsmen, the ferry went to the rescue, pulling the wet and cold kayakers aboard.

However they soon decided to get back in the water and paddle to the island to meet their other, paddleless friend, and wait for the next ferry to take them back.

A witness said the same ferry had approached three kayakers earlier to see if they wanted help on the ferry's way over from Petone, but they were waved off.

Skipper Brandon Leask said he was piloting the ferry away from Petone wharf towards Matiu-Somes Island when he spotted two people in one kayak.

"One of them had fallen out of the kayak and was hanging on to the back of a second kayak," he said.

With their paddles free and drifting away, they were hauled onto the ferry.

The stricken kayakers most likely would have drifted to Matiu-Somes Island but with the cold water and choppy conditions, Leask said he was obligated to change course and rescue the man in the water.

"The guy in the water had been in there for a quite a long time and only had a T-shirt and shorts on so he would have been getting cold," he said.

"I imagine there was probably a bit of inexperience and they didn't look at the weather forecast."

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