Emergency services were called to Holmes Wharf about 9pm yesterday after the 10m-long Jane Marie grounded on rocks near the harbour entrance.
Two people, believed to have been in the sea, were assessed by St John paramedics after the boat began to take on water.
The Otago Regional Council said late this morning there was some evidence of diesel on the water.
Staff trained in oil spill response were at the scene, as there were fears that large surf and an incoming tide, coupled with strong winds, could cause Jane Marie to break up.
Response equipment had been deployed ''with the aim to minimise the impact of any spilt fuel on what is a particularly sensitive environment'', the council said.
''We are liaising with the Department of Conservation and have informed Maritime New Zealand.''
ORC regional on-scene commander Scott MacLean said it was believed the Jane Marie was carrying about 500 litres of fuel, but at this stage it looked "pretty contained".
"A little may have leaked out, but there's nothing that indicates the tanks have ruptured."
The council said the owner of the vessel had engaged a salvage diver from Dunedin, who would locate the fuel tanks with a view to isolating them to prevent any further fuel leaking.
The state of the tanks was not yet known.
Near Holmes Wharf are two penguin colonies and habitats for spotted shags, the Otago shag and white-fronted terns.
Mr MacLean said Doc and the Oamaru Blue Penguin Colony had been informed of the incident, but there was no sign of any impact on wildlife at this stage.
The owner of the Jane Marie had been talking to their insurer, and was waiting for them to arrive to assess the scene and figure out the best way to salvage the boat, Mr MacLean said.
