He said he is unsure if an apology will be offered, the New Zealand Herald reported.
"We will see what happens from here and what other things occur but whether there's an apology, let's wait and see," he said.
Japan alerted New Zealand on Thursday that the ship might enter the area.
On Friday, the ship breached the EEZ to chase an anti-whaling vessel belonging to the Sea Shepherd Conservation Society, Japan's Kyodo reported.
Yasuaki Nogawa, Japan's ambassador in New Zealand, was called to the Ministry of Foreign Affairs and Trade to discuss the incident.
Foreign Minister Murray McCully said the meeting was called to reiterate how disrespectful Japan's actions were.
Nogawa stressed that Foreign Minister Fumio Kishida and his ministry were not part of the decision, the Herald said.