Search for missing boatie in Wellington Harbour

File photo / Hagen Hopkins

A search is underway for a man missing in Wellington Harbour.

The man, aged in his 40s, and his companion were in a small boat off the entrance to the Hutt River just after 5pm when he fell into the water and was swept by the current into the main harbour.

It is believed he was not wearing a life jacket, police said.

An air and sea search began, and a large number of police staff hunted along the shoreline.

"The Hutt River is currently at a very high level and is extremely discoloured due to the outflow of the last periods of rain, making conditions dangerous and underwater visibility nonexistent,'' police said in a statement.

It was understood the two people on the boat were retrieving nets at the time, but the reason for them venturing into that area in such circumstances was yet to be established.

The incident was complicated when Westpac and Airport Fire resources had to be temporarily diverted to investigate a report of a boatie being swept out to sea near Lyall Bay on Wellington's south coast.

At the same time a further report was received of four people who had fallen out of their boat in Titahi Bay north of Wellington, and staff were also deployed to that event.

Fortunately both of these incidents were resolved quickly without issue and the full search of the Hutt River incident resumed, police said.