The incident has led to warnings on Wednesday not to eat fish from North Auckland beaches and also to boaties over the risk of various types of debris that could be floating in the Hauraki Gulf.
The trawler was returning to port when it started taking on water near Moturekareka Island, just south of Kawau Island, just before 9pm on Tuesday.
A spokesperson for the Kawau Volunteer Coastguard said the skipper raised the alarm and turned the vessel towards shore.
However, the trawler sank so quickly only the bow was still above water when the rescue boat arrived.
The two fishermen on board, who were shocked but unhurt, had already made it to safety on a yacht anchored nearby.
The Coastguard crew transferred the men to a second trawler that arrived later at the scene.
The spokesperson said it was "a salutary lesson" that disaster at sea could happen very quickly.
He urged boaties to avoid the Kawau Bay area due a large amount of debris floating on the surface, including nets and boat parts.
Vessels that were caught in a net or holed by floating debris could end up in the same situation, he said.
The call for help came in at 8.49pm and a volunteer crew was at the dock and ready to go within 35 minutes, he said.
He described it as "a great response" on the part of volunteers and also passed on "big thanks to the other boats that helped".
Warning to fishers in North Auckland
Fisheries New Zealand is warning people not to eat fish washing up on North Auckland beaches following the sinking of a fully laden fishing trawler.
Deputy director-general Steve Ham said the boat was carrying a large quantity of fish, mostly snapper, when it sank in 8m of water.
He expected the fish would be seen floating in the area and could wash up at some North Auckland beaches in coming days.
Ham urged people not to collect any dead fish they came across in the area, because they could be unsafe to eat.
He said Fishery officers were monitoring the situation and would be visible in the area for the rest of the week.
Anyone with concerns about dead fish could call the agency on 0800 008 333.
Ham said Fisheries NZ was following up with the skipper, and was relieved both crew members had been rescued unharmed.
Inquiry launched
A Maritime NZ spokesman said the agency had started an investigation into the sinking.
He commended the quick response of the nearby yacht and Kawau Coastguard, which had ensured the safety of the two crew members.
The spokesperson also advised boaties to take any necessary precautions against debris and oil they could encounter from the sunken vessel.
He said the Auckland Harbourmaster was aware of the situation and was responding accordingly.
Maritime NZ would not say if the sinking raised any environmental concerns, such as the potential for pollution from oil leaking from the vessel.
The spokesperson said the response to debris or any oil spill fell under Auckland Transport's responsibility.
RNZ has asked Auckland Transport if there is potential for environmental damage caused by oil leaking from the trawler.
Cause of sinking, environmental risk unclear
A spokeswoman for Coastguard New Zealand said the two fishermen had to abandon the trawler in a life raft and were fortunately picked up by a nearby yacht.
The Coastguard boat Kawau Rescue arrived about 9.25pm, transferred the two fishermen aboard, and performed a welfare check.
Kawau Rescue then rendezvoused with the skipper's son and transferred the two fishermen to his vessel.
The crew returned to their base at Sandspit around 10pm, she said.
It was not immediately clear what had caused the sinking, or if oil on board the trawler posed an environmental risk to the Hauraki Gulf.
The office of the Auckland Harbourmaster would not comment, instead referring questions to Auckland Transport.
