Investigators think the killers navigated tricky waters in a restricted area, dropped the doors of two metal cages and then began firing a high-powered rifle at six trapped sea lions.
The sea lions' carcasses were found Sunday in floating cages moored at the base of Bonneville Dam on the Columbia River.
The animals congregate there to dine on the spring run of endangered chinook salmon trying to get upstream to spawn. Wildlife agents last month started to trap the sea lions and remove the worst offenders.
Only one of the six was among the California sea lions that frequent the dam, said Bob Lohn, regional administrator of the National Marine Fisheries Service. Two were Steller sea lions, which prefer sturgeon over salmon.
The trapping has been suspended.
Veterinarians examining the sea lions Monday were unable to find bullets, said Brian Gorman, a National Marine Fisheries Service spokesman.
He said investigators discounted their earlier theory that the gunshots were fired from the Washington side of the river, about 500 yards away, in part because the cage doors were closed.
Normally, the doors are left open so the sea lions get used to the cages until trappers are ready to remove them, Gorman said.
The traps were next to an island, and investigators theorized Monday that whoever shot the sea lions arrived by boat.
U.S. Army Corps of Engineers spokeswoman Diana Fredlund said the currents are complex and unpredictable as water issues from two powerhouses and the spillway.
"Suffice it to say that in order to undertake (the shootings) this person would have to be somewhat familiar with the trapping methods used there and the operation of the traps," Lohn said.
The trapping started April 24. The federal government gave the states of Washington and Oregon permission to capture or kill up to 85 sea lions a year for five years.
At the request of the Humane Society of the United States, a federal appeals court has disallowed the killing until it hears arguments; a hearing is scheduled for Thursday.
The sea lions removed so far have been sent to zoos and aquariums, although one died before it could be transferred to Sea World.
Both California and Steller sea lions are covered by a federal law that protects marine mammals. The salmon are protected by the Endangered Species Act.
American Indian tribes protecting their fisheries and state governments representing commercial and sport fishermen had promoted the sea lion removal.
"Just as we appeared to have gotten to a working management strategy, this happens," said Charles Hudson, spokesman for the Columbia River Inter-Tribal Fish Commission.
He said the tribes were "deeply disappointed" at the killings and asked for public patience with the trapping. He also said the commission's 14 fisheries agents in the area would aid the investigation by state and federal authorities.
Associated Press writer Jeff Barnard in Grants Pass, Ore., contributed to this report.