Up to 160 pilot whales beached themselves at Toby Inlet near Dunsborough, more than 250km south of Perth, on Thursday.
The Department of Biodiversity, Conservation and Attractions said 29 whales had died.
"We're in the stage of removing them off the beach and taking measurements and samples," Regional Wildlife Officer Pia Courtis said.
The remaining whales that were spread across 500 metres of the beach were helped back out into the ocean where another two pods of about 130 animals were sticking together offshore.
Most of the whales appeared to be adult females with a few calves, Senior Research Scientist Marine Fauna Holly Raudino said.
Whale researcher Ian Wiese was at the "terrible" scene where he saw many of the dead creatures but said considering the sheer number that were on the beach, it was a good outcome.
"When you consider what could have happened here, it has been a really good result," the Geographe Marine Research chair told ABC.
He said it was the biggest stranding event he had ever seen in the area.
But concerns remain that the whales will strand themselves on another beach nearby despite being hauled back into the ocean.
"That often happens but we are hopeful that they will not," he said.
Boats are in the water trying to prevent the pod from stranding again.
"We've got vessels and a spotter plane up in the air doing searches every couple hours to see where they are," Ms Courtis said.
"So far so good they haven't made it back to shore but we will keep monitoring them."
Update on the — Shark Safety WA (@SharkSafetyWA) #pilot #whales stranding in SW WA.The mass stranding has now risen to 50 and 100 pilot whales at Toby's Inlet near #Dunsborough.Experienced staff from #DBCA and #Perth #Zoo #vets are currently being deployed to respond to this evolving situation. pic.twitter.com/5wQeKXSeHZApril 25, 2024
Many volunteers helped to turn the whales so they could breathe and splashed water on their backs while they were beached.
"There were a couple of hundred people who were with the whales, they were trying to comfort and make sure that their heads were out of the water so they could breathe," Mr Wiese said.
"After an hour or so, the ones that were in the water that were still alive went out to sea."
The last mass stranding of whales in WA was at Cheynes Beach in Albany in July 2023 where at least 90 of the mammals died.
In light of the Cheynes Beach stranding and the behaviour of pilot whales, Parks and Wildlife were concerned many of the whales at the Toby's Inlet incident would have to be euthanised but thankfully rescue efforts were successful.
It remains unclear why whales strand themselves.
"No one really understands, the world is puzzled by these sorts of events and I do not think we are very much closer to understanding it," Mr Wiese said.
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