New Zealand on Monday called in Tokyo's ambassador to protest about a Japanese whaling ship entering its exclusive economic zone (EEZ), escalating a diplomatic row over the incident.

Foreign Minister Murray McCully said officials summoned Japanese ambassador Yasuaki Nogawa to express "deep disappointment" at the incursion last Friday.

The complaint to Japan's ambassador comes after the South Pacific nation, one of the strongest critics of Tokyo's whaling programme, had already hauled in the embassy's deputy head of mission for a tongue-lashing.

"Today's meeting with the ambassador served to further reiterate how deeply disrespectful the vessel's entry into our EEZ was," McCully said in a statement.

"New Zealand's strong opposition to Japanese whaling in the Southern Ocean is well known and further action may be taken," he added.

The incident occurred last Friday, when the whaling ship Shonan Maru 2 entered the EEZ as it was pursuing the protest vessel Steve Irwin, operated by the environmental group Sea Shepherd.

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.

While the vessel was legally entitled to sail in the EEZ, the ministry said it had been made clear to Japanese officials before it entered the waters Friday that it was not welcome.

In a statement released late Sunday, it called the decision to ignore New Zealand's wishes "unhelpful, disrespectful and short-sighted".

High-seas confrontations are common between Sea Shepherd's protest ships 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.

Earlier Monday, McCully said 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".

It was "deeply annoying" regardless, McCully said.

The Japanese embassy in Wellington refused to comment on the issue.