Department of Fisheries and Oceans spokeswoman Lara Sloan says tests to determine the cause of death were inconclusive.
She says more tests will be done on the whale, which scientists say would have contributed to its pod for decades.
The loss of the orca identified as J-32 is considered a blow to recovery efforts because there are so few breeding females.
Sloan says the whale that appeared to have been dead for a couple of days was in otherwise good condition, suggesting it may not have been hit by a boat.
J-32 was reported floating near Courtenay and Comox on Thursday and was from the so-called southern resident pods that ply the waters off British Columbia and Washington state.