"It may have dispersed in the very heavy conditions."
Conditions were rough with strong offshore winds when the vessel hit.
The boat, carrying 38 crew and a Ministry of Primary Industries observer, struck rocks while sheltering off an area known as The Neck in Paterson Inlet.
The site is close to the Ulva Island bird sanctuary.
No one was injured and the skipper was able to re-float the boat and steer it to safety.
Sureste 700 is based in Timaru and has been chartered by South East Resources.
The company's manager, Jason Williamson, said the tank was full before the crash, but the skipper was not able to tell how much diesel had been lost.
"I believe the tank is now a mixture of water and diesel."
A diver would inspect the damage tomorrow.
The boat was stable and had been given approval from Maritime New Zealand to make its way to Lyttelton for repairs.
That journey was expected to take about 10 days, he said.