The Arlluk, a federal research vessel that's used by two Alaska Peninsula wildlife refuges, was found submerged at 3:30 a.m. in Kodiak's St. Herman's Harbor.
No one was on board. The cause of the sinking was unknown, Fish and Wildlife Service spokesman Bruce Woods said.
"It's unlikely that they'll be able to speculate as to the cause until after they get the ship up," he said.
Divers were on site, and salvors hoped to raise the vessel by Saturday before a storm moves in.
The Arlluk was carrying an estimated 1,500 gallons of diesel fuel. The Coast Guard estimated no more than 10 gallons spilled.
"That's a lot better than it could have been," Woods said.
Arlluk means "killer whale" in Alutiiq, the language of indigenous Alaska Natives in the Kodiak Island Archipelago, Woods said.
The vessel was built in 1979 and named the Caroline, Woods said. The Drug Enforcement Agency seized it in the late 1990s and used it for about a decade as an undercover vessel. In 2009, the DEA reclassified it as government surplus.
The Alaska Peninsula National Wildlife Refuge and the Becharof National Wildlife Refuge refuges took ownership of the boat that year from the General Services Administration and spent $100,000 refurbishing the motors and foredeck, Woods said.
The boat is 16 feet wide and drafts 6 feet. Refuge staff members use the Arlluk as a mobile field camp to access remote areas, Woods said. It can accommodate a dozen crew and passengers. Researchers also use it to survey marine mammals and seabirds.
"It can be fitted with a 'tuna tower,' which is really handy for spotting sea life or doing marine mammal surveys," Woods said.
The boat has a range of 600 to 700 miles.
The Becharof National Wildlife Refuge is southeast of Katmai National Park at the head of the Alaska Peninsula. The Alaska Peninsula National Wildlife Refuge is farther west on the peninsula. The headquarters for both refuges is in King Salmon.