New Zealand has summoned a senior Japanese diplomat, saying it was "deeply annoyed" after a Japanese whaling ship entered its exclusive economic zone.

Officials in Wellington called in the Japanese embassy's deputy head of mission Friday to make clear their displeasure at the Shonan Maru 2's presence in the EEZ.

The Shonan Maru No 2, one of the security escorts for the Japanese fleet, entered New Zealand's 200 nautical mile EEZ on Friday.

New Zealand's Foreign Minister Murray McCully has called the incursion by the Shonan Maru 2 "unhelpful, disrespectful and short-sighted".

He says the whaling ship followed Sea Shepherd's protest ship Steve Irwin into New Zealand's EEZ and travelled for some distance.

"I did request that the ministry call in the most senior person from the Japanese embassy in Wellington on Friday to convey just how disappointed New Zealand was that a Japanese whaling vessel had come into New Zealand's exclusive economic zone," Mr McCully said

"We asked our people in Tokyo to pass on a similar message to the foreign ministry there."

The foreign ministry said the ship did not enter New Zealand's territorial waters, which extend 12 nautical miles from the coast, but did breach its EEZ, which covers from 12 to 200 nautical miles offshore.

New Zealand's foreign ministry said that the ship "travelled for some distance inside the (EEZ) zone, but stayed well clear of New Zealand territorial waters".

It did not say how long it was in the EEZ.

Mr McCully says New Zealand had earlier made it clear that any such action would be unacceptable.

"The Japanese Government is well aware of New Zealand's opposition to whaling in the Southern Ocean and our strong preference that ships from its whaling fleet do not enter our EEZ," he said.

"While the Japanese vessel has a right to pass through our EEZ, it is disappointing a request not to do so was ignored."

Mr McCully says New Zealand, which is one of the strongest opponents of Japan's whaling programme, would consider further steps "to enable the Japanese to understand just how deeply annoying this is".

He did not specify what the steps might be, saying he was yet to clarify whether the incursion occurred with the blessing of the Japanese foreign ministry or was merely the fisheries agency "flexing its muscles ... without proper regard for the foreign policy consequences".

High-seas confrontations are common between Sea Shepherd and the Japanese, who hunt whales under a "scientific research" loophole in the moratorium on whaling.

In 2010 a collision involving the Shonan Maru 2 resulted in the sinking of Sea Shepherd's speedboat Ady Gil.

New Zealand's foreign ministry said that the ship "travelled for some distance inside the (EEZ) zone, but stayed well clear of New Zealand territorial waters".

It did not say how long it was in the EEZ.

ABC/AFP