Mining company CAP reported on Saturday that the spill occurred at its onshore terminal on Guarello Island, about 240 kilometers north of the town in Puerto Natales, and moved into the waters of the South Pacific, the navy said.
In a statement released Sunday, Greenpeace warned that the consequences could be "devastating" for Patagonia's waters, an area rich in marine life such as whales and dolphins.
The organization said that their habitat could be affected, forcing them to reach the surface of the sea where the diesel had spilled.
"Onboard was a maritime prosecutor to carry out initial proceedings on the causes, the circumstances and those responsible for the dumping of diesel into the sea," said Chilean Admiral Ronald Basasch, reported Reuters.
"The public prosecutor has already issued investigative orders for other public bodies, including the investigative police department in Chile through its environmental force."
CAP, which mines limestone on the island, said in a statement that it initiated its protocol for the incident, which included control and mitigation measures.
Last August, CAP's labor union had already expressed concerns over the environmental policies of the mining company.