The Hawaii Superferry will not sail between Honolulu and the city of Kahului on the island of Maui while the state studies the environmental impact of the interisland ferry service.
State law requires that an environmental study be conducted before service starts, Maui Circuit Judge Joseph Cardoza ruled.
Opponents of the ferry say there is a risk the high-speed boat could strike humpback whales, an endangered species, and otherwise harm the environment.
Hawaii Superferry attorneys told the judge they would appeal. The company's president, John Garibaldi, testified during four weeks of testimony that the ferry would have to leave the islands if the company was forced to wait for the study before starting service.
The Hawaii Supreme Court stalled the Superferry in August when it ruled that state transportation officials should not have exempted the giant catamaran from an environmental assessment required for projects that use state money.
The state is spending $40 million (28.5 million EUR) on ramps and barges needed to load vehicles on and off the ship.
A Kauai judge shot down a legal challenge from residents of that island, but protesters on kayaks in Nawiliwili Harbor prevented the ferry from docking there.
The discovery of the submarine has unveiled a few "inconsistencies." For example, how can one explain the fact that the sub was found where it needed to be searched for from the start?