"It is very possible that she has succumbed at this point and that we may never see her again", Teri Rowles, marine mammal health and stranding coordinator for National Oceanic Atmospheric Administration (NOAA) Fisheries, told journalists during a press phone briefing Tuesday.
NOAA has a plan to try and nurse Scarlet back to health, but it's a complicated one that depends on her condition.
"It's a great relief that she's still alive", said Paul Cottrell, marine mammals co-ordinator with the Department of Fisheries and Oceans.
But veterinarians haven't spotted the 3½-year-old female killer whale in several days.
An aerial photograph of adult female Southern Resident killer whale J16 with her calf (J50) in 2015, when the calf was in its first year of life.
She said it became evident that "we needed to intervene to determine potentially what was the cause and whether there was anything we could do to assist her". The first step, now that she has been recovered, will be a health assessment. This involves collecting breath and stool samples and observing her behaviour.
If a cause can be identified, the veterinarians on board will be able to sign off on the next step-the injection of a long-acting broad-spectrum antibiotic either from a pole or a dart gun. If J50 responds to the salmon, they will be considered as a way to administer medications that may not be injectable. What would be unique is giving the orca medication through live fish, she said.
Rowles said that while the research boats are out in the water searching for Scarlet, they have to keep a distance at least 200 yards to make sure that they don't further stress the sick, young whale or other whales.
Rowles said such imagery has shed more light on the whales' overall body condition and growth over time.
This is the largest rescue effort of a killer whale along the Canadian and American coast since 2002, when an orphaned northern resident killer whale known as Springer was captured and moved.
There are now only 75 southern resident killer whales that live in the waters along the US west coast from Alaska to California, according to Ken Balcomb of the Center for Whale Research.
Springer was two years old when she was found in Puget Sound near Seattle, ailing and separated from her pod.