A man found in the water clinging to a floating container for several hours overnight after the boat he was in overturned has been rescued.

Two men were rescued after their boat overturned late Saturday night. Photos: supplied.

Two men were returning from a fishing trip at Mayor Island at 11pm on Saturday when their vessel overturned late Saturday night.

An Auckland Rescue Helicopter Trust spokesperson says a crewmember managed to swim to shore to raise the alarm.

An Auckland Westpac Rescue Helicopter was deployed from its Whitianga base to the scene, where a search found the missing crewman clinging to a container.

A Waihi Beach Coastguard vessel was vectored to the man's position where he was uplifted by the helicopter and taken to shore, before he was transported to Thames Hospital.

Initially, specialised search equipment Night Vision Goggles were used to locate the missing man.

Auckland Rescue Helicopter Trust is believed to have received a call about the missing man about 5.30am.

The boat is reported to have been spotted just before 6.30am, while the man was discovered about 200m from the vessel.

A SunLive reader says a helicopter landed in a carpark by the coastguard building at Bowentown after rescuing two people.

'The ambulance arrived to check them out, but they weren't taken away.”

In a media statement,Hamilton Police Senior Sergeant Robbie Hermann says the two men are lucky to be alive after a fishing trip went horribly wrong.

At about 11pm on Saturday the two men, aged 40 and 26, were heading home after fishing near Mayor Island.

"While attempting to cross the Bowentown bar, the 7.0 metre aluminium boat they were in was struck by a rogue wave capsizing the boat.

"The men clambered onto the upturned boat as it drifted into the harbour on the incoming tide. Neither man was wearing a life jacket."

He says after a few hours, and when the tide changed, the men decided to try and swim to the shore.

"One man made it to land and was able to find someone with a cell phone at which point Police and Coastguard were contacted."

The second man who was not a strong swimmer tied himself to a plastic fuel container with the drawstring of his shorts. He had been floating like that for six hours.

A significant rescue effort was in put in place which involving two helicopters, Coastguard rescue boats and IRB's from the Waihi Surf lifesaving club.

At about 6.40am the second man was spotted by crew on one of the helicopters. A Coastguard vessel located the man and took him to shore. The man was suffering from mild hypothermia.

This event could have so easily ended in tragedy. Police and Coastguard repeat the advice about the wearing of life jackets and the use of trip reports where the details on the planned journey are logged with the Coast guard.

With the help of the Auckland Westpac Rescue Helicopter and boats from Whangamata and Tauranga, Waihi Coastguard's Gallagher Rescue boat was able to rescue the missing man, who was clinging to a floating fuel container, around dawn, on Sunday.

Waihi coastguard skipper Tim Watts says both men were lucky to be alive, with the second only suffering from mild-hypothermia. He was taken to hospital.

"He was very thankful that we got there. He was a bit concerned but okay.

"It could have been a lot worse."

The Bowentown bar is notoriously difficult to cross and the conditions of the water on Saturday night weren't ideal, says Tim.

"Without experience you should not take on our bar at night time and I don't think they had a lot of experience crossing a bar.

"I know we had breaking waves coming over when we were going out to look for them."

The pair, a 40-year-old and 26-year-old, had been out fishing in a seven metre, aluminium, Blue Fin boat. Tim and his team towed the boat back to shore and hoisted it onto the men's trailer. They were off the water by 9.30am.

Waihi Coastguard media officer Monique Caddy says the boat overturned on the bar at Bowentown on Saturday evening.

"Volunteers were called out around 3am this morning. We picked up one survivor that had been spotted by the rescue helicopter."

Police and Coastguard repeat the advice about the wearing of life jackets and the use of trip reports where the details on the planned journey are logged with the Coastguard.

Additional reporting: stuff.co.nz