Police boarded a protest ship and arrested the skipper following "grave concerns" for the safety of the crew of Ocean Explorer off the coast of East Cape.
Protests over the Brazilian oil giant Petrobras's ship heated up when police from a patrolling navy boat boarded San Pietro, which is owned by local iwi.
A Police spokesman said the arrest of skipper Elvis Teddy came after a blatant breach of safety by the boat.
"This followed repeated warnings to the boat about activity it was engaged in that was causing grave concerns to the master of the Ocean Explorer," he said.
Police could not go into further detail of what activity was being carried out by the protest vessel or what the skipper would be charged with.
San Pietro was being sailed by the remaining crew on board.
The boat is owned by East Coast iwi Te Whanau a Apanui and is part of the flotilla that includes Greenpeace.
In a statement, Greenpeace defended the actions of the San Pietro crew.
"The crew of te Whanau a Apanui’s fishing boat San Pietro went fishing at a safe distance in front of the deep sea oil survey ship, Orient Explorer."
Whanau a Apanui tribal leader Rikirangi Gage radioed the Captain of the Orient Explorer and said he was not welcome in the iwi's waters.
"This is not a protest. We are defending tribal waters and our rights from reckless Government policies and the threat of deep sea drilling."
Police approached the ship on two inflatable boats.
Police issued maritime notices last week requiring the Greenpeace flotilla to remain at least 200 metres from the two ships. Protestors face a fine of $10,000 or up to 12 months' jail for breaching the notice.
The navy's patrol vessel and air force aircraft, including an Orion, have been working with police to monitor the protest.
The Orient Explorer is doing the first seismic study of the Raukumara Basin area off the East Coast since Petrobras was awarded a US$118 million (NZ$151m) five-year permit last June.
Petrobras has earlier warned action off the East Cape could prompt it to withdraw early from its contractual obligations.
- Fairfax Media