Brazilian state-owned oil company Petrobras is planning to conduct seismic testing for oil sediments in the Raukumara Basin after it last year bought a five-year permit to explore the area.
Greenpeace said swimmers from a protest flotilla of five vessels entered the water today and diverted the oil survey ship the Orient Explorer off course.
Acting Energy and Resources Minister Hekia Parata said the protestors came dangerously close to the ship, which made it unsafe to continue the research.
It was disappointing protestors had disrupted the research and Ms Parata urged them to take a calm and reasoned approach towards the company's rights.
"Democracy protects the right to protest but not to the extent of interfering with others' rights," she said.
Oil and gas exploration could contribute significantly to the New Zealand economy, Ms Parata said.
"A number of these protestors will sail off leaving the local people no better off socially or economically."
But Greenpeace climate campaigner Steve Abel said protesters were sending an "emphatic message" to the Government that deep sea oil drilling would not be tolerated in the country's waters.
"If we don't stop this initial deep sea oil exploration, rigs could be off coasts all around New Zealand in the near future, each one increasing the risk of spills and fuelling climate change as the oil is burnt."
The flotilla was supported by East Cape iwi Te Whanau a Apanui, which said the company had no right to be in the waters east of their tribal lands.
"This is not a protest," iwi spokesman Rikirangi Gage said.
"This is an act of defence of our ancestral lands and waters that have sustained us for generations."
Police were monitoring the situation.
