Hawaii Superferry Inc. halted service after the Coast Guard advised that it could not assure safe passage of the 350-foot ferry in and out of Nawiliwili Harbor on Kauai, where a flotilla of protesters blocked it from docking late Monday.
A court order sought by environmentalists had already halted service to Maui, with a hearing set for Wednesday.
Gov. Linda Lingle, a longtime ferry supporter, also requested Tuesday that the service be suspended because of public safety concerns.
Opponents say the ferry endangers whales, threatens to spread invasive species and will worsen traffic and pollution. But Superferry officials say the ship's water jet propulsion system means there are no exposed propellers to strike aquatic animals.
John Garibaldi, Superferry's president and chief executive, said operations will not resume until safety is assured. The company, which invested $300 million to launch the service, could lose millions while its vessel is grounded.
"The cost to us really isn't very important," he said. "It's really making sure we can take care of our passengers."
Lingle said she was concerned by protests Monday night on Kauai that led to 11 arrests after about 65 people on surfboards, canoes and kayaks formed a human blockade and forced the $95 million ferry to turn back to Honolulu.
The ferry, named Alakai, was stalled outside Nawiliwili Harbor late Monday for nearly three hours as Coast Guard vessels, including an 85-foot cutter, failed to clear the way for the ship.
The ferry returned to Honolulu about midnight, and some passengers, who had paid a discounted $5 fare for the voyage, were put in hotels and given vouchers for future travel.
The company also paid for flights, hotel rooms and car rentals for passengers who sailed and were stranded on Kauai on Sunday.
For decades, the only way to travel among the islands - where an estimated 1.3 million people live and tens of thousands of tourists arrive each day - was by the local airlines.
Austal USA, which built the ferry in Mobile, Alabama, is building a second, scheduled to serve the Big Island starting in 2009.