Plans for a new mine for ore that contains copper, zinc and gold have caused alarm among scientists and indigenous people

The green-lighting of the world's first deep-sea mineral mine in Papua New Guinea waters has caused alarm among scientists and indigenous people who fear it will damage local marine life.

Papua New Guinea's prime minister, Michael Somare, today licensed the new mine for ore that contains copper, zinc and gold, to be run by Canadian company Nautilus Minerals. Sited in the Manus Basin within Papua New Guinea's territorial waters, it will be near hydrothermal vents 1,600 metres below the surface.

Driven by rising copper prices around the world, Nautilus' Solwara 1 project will excavate 1.2 to 1.8m tonnes of high-grade sulphide ore a year.

Scientists are concerned about the scale of the mining. Paul Tyler from the University of Southampton and chair of the Census of Marine Life said: "Hydrothermal vents have a very distinctive fauna that is only found on hydrothermal vents so mining close to the vents could wipe out the vents or cause a large amount of damage in the surrounding area."

Nautilus says it has carried out extensive environmental research and impact assessments, and has conservation mitigation strategies in place such as moving organisms for later recolonisation. But Tyler said: "When you mine near a hydrothermal vent you change the flow of fluids through the sea floor. You might switch the vent off or create another one elsewhere – that might affect the distributions of animals around the vent." Deep-sea organism populations do not have resilience to disruptions and have slow grow growth because of limits in food supply and the cold water.

"These organisms catch, store and break down carbon that is removed from the atmosphere by shallow water organisms," said Elliott Norse, president of Marine Conservation Biology Institute in Washington DC. "The deep sea also harbours organisms that could be important to humans as anti-cancer medicines – but that we might not even know about yet."

The indigenous communities of Papua New Guinea are also against the mining operation, and have petitioned the government to prevent it.

However, one expert said the risks had to be put into the context of damage caused by other types of mining, such as excavating a mountaintop. Linwood Pendleton, the director of Ocean and Coastal Policy at Duke University, said: "Hydrothermal vents are naturally combustible habitats, they blow up, they become colonised, then the vents die and the ecosystems around them die, so if mining were done at a small scale and low frequency then it may fit very well into this chaotic system of destruction. Mining a mountaintop, once it is gone, it's gone."

It is unlikely that concerns will stop the mining project going ahead as no one from the international community can interfere in Papua New Guinea's territorial waters of the Bismark Sea.

Comment was not available from Nautilus Minerals.

• 22 October update: The expected announcement of the go-ahead for Solwara 1 to the national media of Papua New Guinea did not occur yesterday. No official reason was given for the deferral of the licensing.