A man had to be flown to hospital after accidentally stabbing himself while cutting a shark off his fishing line.

The commercial fisherman, who was in his 40s, had been out at sea in fairly rough seas on Monday when he caught a blue shark, Auckland Westpac Rescue Helicopter paramedic Chris Deacon said.

While trying to cut it off the line he accidentally stabbed himself with his filleting knife.

"They had been at sea for a few days and there was a reasonable-sized swell and they were fishing for blue-finned tuna when they pulled up a blue shark which was quite large, and he was trying to cut it off his line," he said.

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"With the roll of the ship he stabbed himself."

The man waited for treatment until the boat reached Great Barrier Island yesterday. He was treated by St John staff in Port Fitzroy before being flown to Auckland Hospital, just before 3pm, with moderate injuries.

Of the man's decision to wait until getting to shore the next afternoon, Deacon said he probably did not want to bother anyone.

"They are a fairly hardy bunch, fishermen," he said.

"He probably assessed he didn't need immediate care - but he certainly needed care."

Deacon said the man and his colleagues had done everything right by putting a compression bandage on the wound, which he described as "moderate", until the ship reached port.

Although the Auckland Westpac Rescue Helicopter could have winched the man from the ship if necessary, there were always risks associated with that, Deacon said.