But she later turned up and was seen with her family.
The Department of Fisheries and Oceans in Canada and the National Oceanic and Atmospheric Administration in the USA launched a massive cross-border search effort Thursday. The West Coast Marine Mammal Stranding Network has been alerted.
The hotline for stranding reports is 866-767-6114.
The DFO said teams were standing by in case J50 required medical treatment.
The Center for Whale Research said that the orca and her group became separated from the main pod somewhere in the Strait of Juan de Fuca.
"Watching J50 during the past three months is what extinction looks like when survival is threatened for all by food deprivation and lack of reproduction", the center's statement said. "We have seen all the other members of her family during these outings".
The center added: "The message brought by J50, and by J35 and her dead calf a few weeks ago, is that the [southern resident killer whales] are running out of reproductive capacity and extinction of this population is looming, while the humans convene task forces and conference calls that result in nothing, or worse than nothing, diverting attention and resources from solving the underlying ecological problems that will ultimately make this once-productive region unlivable for all". But no one has seen her in days.
The high-profile cases have focused worldwide attention on the plight of southern resident killer whales, whose numbers have dwindled to 75 and now - if J50 has died - to 74 in three pods. The pod has not produced viable offspring in three years.
The orcas have struggled with pollution, boat noise and, most severely, a lack of their preferred prey, chinook salmon, because of dams, habitat loss and overfishing.
Officials had hoped that J50, born in December 2014, might eventually reproduce and assist with the species' recovery.
NOAA has prepared plans to capture J50 if she can be taken from her pod safely or is otherwise stranded or alone.
"I thought she was dead Monday", Balcomb said.
Researchers have been monitoring J50 since noticing her emaciated state. As teams scrambled to find her Thursday, she failed to appear with her pod once again, despite favorable sighting conditions.
With J50′s presumed death, there are now just 74 southern resident orcas left in the wild. The search at this point is just a matter of protocol, he said.
"(She) definitely captured our hearts, but I don't want to leave you with any false hopes, this is a very sick whale", he said.