The search for an elderly man missing in Manukau Harbour continues today without the Police National Dive Squad.

The 74-year-old man was thrown into the water when the boat he and another man were in capsized around 5pm on Thursday.

Police said the Eagle Helicopter would continue to do aerial sweeps of the area throughout the day today.

At low tide this afternoon a police search and rescue team will attempt a shoreline search between Hamilton's Gap and the South Head Lighthouse, police said.

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However, treacherous sea conditions has prevented the Police National Dive Squad from returning to search in the area the man was last seen.

The divers have been to the location, but it was deemed unsafe due to very little visibility and swift currents.

The missing man was one of two men in an 18-foot boat which overturned while crossing the Manukau Bar.

Friends on a nearby boat managed to pull one man from the water unhurt, but the elderly man did not surface.

Police believed both men were wearing life jackets.

Senior Constable Garry Larsen of the police maritime unit said everyone in the group was upset and the people in the boat which rescued the other man were friends of the missing man and his family.

"They were all going together," he said. "The boat that capsized was following them."