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.
Acting Energy and Resources Minister Hekia Parata said the protesters came dangerously close to the ship, which made it unsafe to continue the research.
It was disappointing protesters 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 protesters will sail off leaving the local people no better off socially or economically."
