A fishing vessel has ran aground and sunk near the Oamaru Harbour entrance, spilling oil in one of the coast's most sensitive environments.

However, the spill does not seem to be threatening nearby penguin and bird colonies.

The 11m Jane Marie ran aground last night.

Two crew ended up in the water and were taken to hospital suffering from hypothermia, a Maritime New Zealand spokesman says.

Otago Regional Council and Department of Conservation staff were in Oamaru on Friday morning to contain any spill and to monitor any effects on the penguin colony and seabird nesting sites.

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"They have found, fortunately, very little oil and debris. There doesn't seem to be any danger to the birds," the spokesman told NZ Newswire.

A council spokeswoman says there was an odour of fuel but there were no indications there had been a serious spill.

It was not yet clear what caused the sinking.

A Maritime NZ officer, now at Port Chalmers investigating the death of a cruise ship crewman, will travel up to Oamaru later on Friday to investigate.

An insurance assessor is expected to determine best way to salvage the vessel.