A spokesman said the boat was coming into Oamaru Harbour late on Thursday night and ran aground on rocks on the seaward side of Holmes Wharf.
He said the two crew on board ended up in the water, were rescued and went to hospital for treatment.
The man believed to be the owner of the boat did not want to talk about the experience, but was pleased there was no loss of life.
Otago Regional Council on-scene commander Scott MacLean said it was believed Jane Marie was carrying about 500 litres of fuel.
"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 hired a salvage diver from Dunedin, who would locate the fuel tanks with a view to isolating them to prevent any further fuel leakage.
Response equipment was set up around Oamaru Harbour to collect any spilt fuel in what is a particularly sensitive environment. Near Holmes Wharf are two penguin colonies and habitats for spotted shags, the Otago shag and white-fronted terns.
A crane was also brought in later in the day to help with the recovery efforts.
Oamaru Blue Penguin Colony research scientist Philippa Agnew said the day was spent waiting and doing surveillance of the local bird life with Oamaru Department of Conservation staff.
"Just making sure there aren’t any birds covered in diesel coming in. There haven’t been so far.
"There’s a relatively small amount of diesel in the water. We’ll just continue to observe things as the night wears on."
She said the colony’s rehabilitation facility was ready to take any sick or diesel-covered birds.
"If the public have any concern or see birds with diesel just give the penguin colony a call."
A regional council spokeswoman said the boat was secured overnight and should be removed sometime today.
● The colony’s phone is manned from 9.30am to 11pm. (03) 433-1195.
