The killer whale belongs to group that has been blighted by pollution, boat traffic disturbances and, worst of all, a lack of the salmon they rely on for food.
Dr Ken Balcomb, of the Centre for Whale Research, said: “We’re watching a population marching toward extinction.
“Unless we do something about salmon recovery, we’re just not going to have these whales in the future.”
The news means there are only 74 whales remaining in the group, which has failed to produce any offspring in the past three years.
Dams, habitat loss and fishing have all contributed to the decline in salmon populations, which has had a disastrous knock-on effect for the whales.
The orcas are in such bad shape that experts prepared last-ditch efforts to save the emaciated three-year-old known as J50.
A veterinarian fired an antibiotic-filled dart into her, crews dropped live salmon in front of her to try to get her to eat, and scientists even mulled capturing her so they could diagnose and treat her.
Despite their efforts, J50 has not been seen since last Friday.
As teams scrambled to find her on Thursday, she failed to appear with her group once again, despite favourable sighting conditions. Dr Balcomb, who tracks the whales for the US government, declared her dead late on Thursday afternoon.
Michael Milstein, a spokesman for NOAA Fisheries, said the agency gives great weight to Dr Balcomb’s assessment of the whales, given his long experience monitoring them. But, he said the US and Canadian governments plan to continue searching Friday on the chance she is still alive.
“We want to make the most of it to make sure that if J50 is there, we haven’t missed her,” Mr Milstein said.
“We haven’t given up hope.”
Crews in a US Coast Guard helicopter, 10 vessels, whale watch crews and other resources on both sides of the border were involved in the search. Authorities also alerted a network of people who respond when marine mammals wash ashore.
Whale experts feared the orca was dead earlier this month when J50 lagged behind her family and went missing. But she later turned up and was seen with her family.
Orcas have been struggling in recent years, and experts reckon their numbers are now at their lowest in more than three decades.
A recent victory for the whales came when the approval of the controversial Trans Mountain pipeline expansion in Canada ground to a halt after a federal court ruled the marine predators had not been properly considered.
A whales from the same group as J50, known as J35, made international headlines in August when she carried the corpse of her dead calf with her for over two weeks.
Additional reporting by AP