An ailing killer whale calf that scientists have been trying to treat since August has died, scientists believe.

Ken Balcomb, head of the Center for Whale Research on San Juan Island in Washington state, said research teams declared the three-year-old female, known as J50, dead on Thursday evening.

J50 had not been spotted since last Friday.

Scientists became concerned for the southern resident killer whale in early August, when overhead photography showed she had lost 20 per cent of her body weight. The images triggered a cross-border emergency response and an unprecedented attempt to shoot the whale with doses of antibiotics.

"We know we're not going to get a carcass, because she was so thin her body sank to the bottom for sure. We're calling her dead as of 5 o'clock this [Thursday] evening," Balcomb said.

"Our boat is returning with no evidence that she's alive anywhere in the population."

The southern resident killer whales, which are so endangered there are just 75 left, swim between Canadian and U.S. waters through busy shipping lanes.

J50 was part of the same family group as a mother orca who gained international attention earlier this year for carrying her dead newborn, in an apparent display of mourning, for 17 days.

J50 and her mother J16, are seen together on Aug. 7. (Fisheries and Oceans Canada)

Balcomb said when J50 was last seen she was suffering from "peanut head" — a condition characterized by the fat behind her skull becoming severely depressed.

"We've never seen a whale recover from that sort of emaciation," he said, adding that scientists were not ultimately able to determine why the whale was so thin.

"But we know all of the whales are looking pretty slim, there is a problem with the prey resource, Chinook salmon, in the entire Pacific Northwest."

Balcomb said the presumed death of J50 is a symptom of a much larger problem.

In the past 10 years, 42 whales have died, and only three have been born.

"The loss of one whale is tragic, but the loss of reproduction in the entire population is catastrophic," he said.

"We are witnessing a slow-motion extinction here."

The U.S. coast guard is continuing to conduct aerial and boat searches for the whale in U.S. and Canadian waters.

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