Carter said on Monday that New Zealand had an obligation on humanitarian grounds to respond to the Japanese government's request for help to rescue the man.
"There were issues around the sensitivity and security and secrecy of his arrival so it required some dialogue with the Japanese Embassy, but in the end they asked and we agreed," he told New Zealand Radio.
The whaler was flown to New Zealand hospital on Sunday and is reported to be in stable condition. His illness has not been disclosed.
Japan will pay all costs of the crewman's transport and rescue.
|Japan plans to harvest 900 whales|
this season [GALLO/GETTY]
New Zealand has staunchly opposed Japanese whaling but Carter said the government had an obligation to help when a life was at risk.
"There are people who feel very passionately, I'm one of them, I guess, against Japanese whaling. New Zealand's taken a very strong stand on it," he told New Zealand radio.
Japanese whaling ships are barred from docking in New Zealand ports and the whaling vessel in question was not allowed to enter New Zealand's territorial waters last week.
The ship was met outside New Zealand's 19-km exclusion zone by a rescue helicopter.
|Japan says sales of whalemeat help to fund |
scientific research [GALLO/GETTY]
Carter's ministry recently released footage taken by a New Zealand Air Force surveillance aircraft of the Japanese fleet harpooning and processing whales in the Southern Ocean.
It refused to release the coordinates at which the fleet was filmed to Greenpeace and other environmental groups, who plan to intercept the whaling vessels and hamper their operation.
A global moratorium on commercial whaling has existed since 1986 but Japan kills hundreds of whales each year under a scientific whaling programme.
It is trying to get the moratorium lifted and has called for a special meeting of members of the International Whaling Commission this month but 26 anti-whaling nations have said they will boycott the meeting.
Japan plans to harvest more than 900 whales this season as part of the programme.