The Government is confident there has been no change in Japan's whaling policy, despite recent action by Japanese whalers in the Southern Ocean.
A Japanese ship followed a protest vessel into New Zealand's Exclusive Economic Zone last week, despite the New Zealand embassy in Tokyo saying that was unacceptable.
Since then, two senior Japanese diplomats have been summoned to the Ministry of Foreign Affairs in Wellington, where New Zealand has expressed its deep displeasure at the action.
Foreign Affairs Minister Murray McCully said he was reluctant to believe Japanese foreign affairs officials were behind the decision to enter the zone.
"We're trying to work out what's happening inside what is quite a big and sometimes cumbersome system."
Sometimes the fisheries agency, which had always been a significant player in the Japanese administration, made their own foreign policy decisions, Mr McCully said.