Earlier this year, whale hunters and environmentalists clashed in the Southern Ocean.
A high-speed environmentalist vessel, the Ady Gil, and a Japanese security vessel collided, in a culmination of weeks of tension over whale hunting.
After the incident, the captain of the damaged trimaran, Pete Bethune, boarded the Japanese ship, Shonan Maru 2, to deliver a letter of protest.
He was then held on board the vessel for just under a month, taken back to Tokyo and arrested by Japanese authorities on Friday morning.
The New Zealander is expected to be charged with trespass.