"Experts found that the whales died during the night," Marian Bestelink, a spokesperson for the ministry of economic affairs, told AFP.
"We are going to investigate why they beached and then we will remove them," Bestelink said, adding that the process would probably take several days.
The animals became stranded on Tuesday on a beach on Texel, an island off the northwest Dutch coast. Experts said the beached whales had already been badly injured and their chances of survival were poor.
Volunteers tried to save them but called off their efforts late in the night because of bad weather and darkness, ANP news agency said.
The sperm whale is the largest of the toothed whales, and the largest toothed predator. It can measure up to 20 metres (67 feet) long and weigh over 50 tonnes.
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