Two men are lucky to be alive when a fishing trip went horribly wrong after their boat was hit by a rogue wave crossing Bowentown bar at 11pm last night.

Neither were wearing lifejackets, leaving them to clamber on to the upturned hull of the capsized 7m aluminium boat as it drifted into the harbour on the incoming tide.

The men aged 40 and 26 stayed put until the tide turned and sucked the boat past Anzac Bay.

They decided to strike out for shore, with the younger stronger swimmer making land while the older man took the precaution of using the drawstring of his shorts to tie his wrist to a yellow 20-litre petrol container.

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He failed to make the shore and was sucked out to sea.

The man who made the shore raised the alarm at about 3.50am.

Waihi Coastguard launched Gallagher Rescue and went into a search pattern where they assumed the man would be.

Westpac Rescue Helicopter spotted the man clinging to the yellow drum at 6.40am, about 200m away from where he would have been found by the coastguard's search pattern.

Senior Sergeant Robbie Hermann of Hamilton Police said the rescue involved a significant effort including two helicopters, coastguard rescue boats and IRB's from the Waihi Surf Lifesaving Club.

Gallagher Rescue said the man was still quite lucid and in surprisingly good shape when they picked him up. He was wrapped him in a rescue blanket and taken back to a waiting ambulance at Anzac Bay where he was treated for mild hypothermia by St John paramedics.

Mr Hermann said the event could have so easily ended in tragedy.

Police and Coastguard repeated advice to wear life jackets and use trip reports so that the details of planned journey were logged with Coastguard.

The capsize happened as the men, understood to be from Katikati, were returning to Anzac Bay after a fishing trip to Mayor Island.

The Auckland Westpac Rescue Helicopter received a call about the missing fishermen from Waikato SAR Police at 5.30am. Westpac Rescue 1 took off from Coromandel Rescue Helicopter Trust at Whitianga for the search.

The boat was recovered and towed back to its trailer at Anzac Bay.