The pod of almost 100 long-finned pilot whales was spotted in shallow water off Cheynes Beach, about 400 kilometres (250 miles) southeast of Perth on Tuesday.
Fifty-one of them died overnight, despite the efforts of volunteers and staff from the state’s Parks and Wildlife Service.
Late on Wednesday afternoon, incident controller Peter Hartley said the surviving whales were being monitored and, once they have been assessed as being strong enough, they would be released.
Mass strandings of pilot whales are not uncommon in Australia and New Zealand.
Last October, approximately 500 pilot whales died when they beached on the remote Chatham Islands in New Zealand.
Scientists do not fully understand why mass strandings occur, but pilot whales, which can grow to more than six metres (20 feet) long, are highly sociable, so they may follow pod-mates who stray into danger.