"Our staff responding to the stranding at Farewell Spit have confirmed that 9 of the stranded whales have died and 40 are still alive", the department wrote on Facebook.
The department added that 65 volunteers helped to care for the surviving whales until they could be refloated to deep waters.
"We have about 65 volunteers assisting with the stranded whales currently. We do not need any more volunteers at this time", the department said.
Pilot whales belong to the family of oceanic dolphins, but their behaviour is considered more typical of larger whales.