Japan's top diplomat in New Zealand has been called to account over a whaling ship sailing within the country's exclusive economic zone (EEZ).

Prime Minister John Key has confirmed the Japanese ambassador, Yasuaki Nogawa, was summoned today to the Ministry of Foreign Affairs, just three days after his deputy head of mission received a similar message.

"What the New Zealand Government has done is made it quite clear to the Japanese we didn't appreciate them going into our EEZ," Key said.

The Government would "wait and see" over whether Nogawa would be summoned to the Beehive.

Foreign Affairs Minister Murray McCully slammed the incursion as "deeply disrespectful" saying it had "caused offence".

McCully said he had been advised the Japanese vessel Shonan Maru 2 followed Sea Shepherd protest ships deep into New Zealand's exclusion zone.

He said that on his instruction, New Zealand embassy officials in Tokyo had made it clear to Japan that any incursion into New Zealand's EEZ would be unwelcome.

Japan's whaling fleet ignored that, chasing the Sea Shepherd's Steve Irwin for some distance inside the zone. The ship stayed clear of New Zealand territorial waters.

"While the Japanese whalers' decision to ignore New Zealand's strong wishes in this respect has no legal implications, clearly it was deeply disrespectful," McCully said.

"The seas within the New Zealand EEZ, between 12 and 200 nautical miles, are not New Zealand territorial waters.

"The New Zealand Government has no legal means of excluding any vessel from entering. By contrast we have some legal capacity to exclude vessels from within our territorial waters, 12 nautical miles from the coast."

Key would not be drawn on what options were available if Japanese whalers moved into New Zealand's economic waters again.

"It's not the most serious issue in the world, but were opposed to their scientific whaling in the Southern Ocean, and we've made that quite clear."

Key said New Zealand had a strong relationship with Japan in other areas.

On Friday the Ministry of Foreign Affairs called in the deputy head of mission, the most senior representative present at the Japanese embassy in Wellington that day, to answer questions and hear New Zealand's view.

"The ministry conveyed the deep disappointment of the New Zealand Government that Japanese whalers had been insensitive to the views of New Zealanders by entering New Zealand's EEZ against our wishes," McCully said.

'DO MORE OVER BREACH' - OPPOSITION

Labour and the Greens are calling on the Government to up the ante on Japanese whalers who breach New Zealand waters.

Labour's foreign affairs spokesman David Shearer said the report of the breach was a worrying development in the confrontation that is going on in the ocean south of New Zealand.



"While I accept we have no legal right to exclude the Shonan Maru 2, Murray McCully must keep up the pressure on Tokyo.



"The fact that the Japanese Government was aware, and appeared to sanction, the ship's entry into New Zealand's EEZ, when it knew of New Zealand's continued opposition to whaling is deeply concerning."



Shearer commended McCully's summoning of Japan's top diplomat to answer questions over the Shonan Maru 2's unwelcome entry as a "good first step".



"But he needs to ensure that the Japanese Government is left in no doubt that New Zealanders see this move as deeply disrespectful. The Government must continue to hold Tokyo to account for this act."

The Green Party said the Government needed to do more than just express disappointment.



"It is offensive that Japanese whalers are in New Zealand waters. The Government should lodge a formal diplomatic protest through the New Zealand Embassy in Tokyo," said Green Party oceans spokesman Gareth Hughes.



He said McCully should Australia's suit, by lodging a formal protest with the Japanese Government.



"Earlier this month, the Australian Embassy in Tokyo passed on a diplomatic protest to the Japanese Government over a whaling support vessel entering Australia's EEZ.



"New Zealand can act like Australia has and lodge a protest in Tokyo," Hughes said.