Those involved were not named last night because next of kin had yet to be informed of the deaths. But police confirmed members of the public rescued the three survivors and recovered the two bodies.
Two of the three survivors, a 41-year-old and 49-year-old, were flown to hospital by rescue helicopter while an ambulance took the third to hospital.
The boat had not been found last night. "It could be at the bottom of the ocean," Inspector Andrew Brill said. "We just don't know yet."
Auckland Rescue Helicopter doctor Cameron Rosie said the rescue chopper landed at Whatipu Beach, on the outside of the bar, where Dr Rosie assessed the three survivors.
"They were shattered physically, really exhausted and really cold," Dr Rosie said.
He said it appeared the boat had encountered difficulties while attempting to re-enter the harbour.
The bodies of the two men who died were taken to Little Huia Bay.
The men involved in yesterday's tragedy were in the water for up to two hours.
Had Coastguard been notified it would have begun a search after 30 minutes in the absence of a call confirming the bar had been safely crossed, Coastguard Northern Region duty officer Carolyn Caukwell said.
An Auckland Council regulation introduced this year made the wearing of lifejackets compulsory on boats under 6m unless the skipper had granted permission to remove them.
It followed a string of tragedies on the water, including the 2012 drowning of So'saia Paasi and his 7-year-old son, Tio, after a dinghy capsized at Mangere Bridge.
Mangere Boating Club Commodore Keith Hedges said conditions at the bar over recent days had been "flat-as".
"The guys went out [on Sunday] and it was dead flat."
Notifying Coastguard of a pending bar crossing attempt was mandatory for all members, Mr Hedges said.
In 2010 a 50-year-old fisherman died and three others spent almost eight hours clinging to their upturned boat after it capsized during an attempt at crossing the bar.
The harbour entrance is also the scene of the worst shipwreck in New Zealand history when 189 people drowned after the HMS Orpheus sank in 1863.
Five people have died in water-related incidents this holiday period, while a teenager who was swept out to sea in the Far North on Saturday remains unaccounted for.
Manukau Harbour's narrow mouth means the flow of water can be very rapid. At high tide, the bar is about 2m below the surface. But because of its shape and shifting location, it can be unpredictable.
Stranger comforts mum of drowned teen
The mother of a teenager swept out to sea in Northland on Saturday was comforted by a stranger as she stood on the beach in anguish, watching the frantic search for her son.
The stranger, Auckland woman Rutu Pandya, is still praying the 16-year-old will be found, and is deeply affected by his family's pain.
She was at 90 Mile Beach at Hukatere in the Far North with her husband and a friend when the tragedy unfolded.
"The boy's mother was absolutely frantic, in tears."
Mrs Pandya did the only thing she could think of to help. "I just put my arms around her and hugged her ... What do you say to a person who has just lost their child?"
The teen was swimming with family when he was swept out to sea. A search produced no sign of him.
Mrs Pandya has not been able to stop thinking about the boy and his family. "When you see someone in that much pain, you never get over it."
Police and volunteers scoured the shoreline for the teen's body yesterday. Far North Rescue chairman Dave Ross expected the search to take up to three days.
The suspected drowning is one of several water tragedies this holiday period. On Boxing Day 47-year-old Simon Camp died at Karioitahi Beach, 70km southwest of Auckland, while surfing on a board he got for Christmas, police said.
On Christmas Day Heng Li, 25, died at Northland's Uretiti Beach, and Imogen Saleupolu-Mataafi, 1, is believed to have drowned in a pool set up in her family's Manurewa backyard. Anna Leask, additional reporting:
- NZME.
