The pod of nine whales became trapped on mudflats at low tide in the Swale estuary near Sittingbourne on Monday night. One whale was found dead on Tuesday morning, while three others were confirmed dead just before 15:00 BST.
A rescue operation to save the stranded whales was called off after "varying inaccurate reports of the location", the British Divers Marine Life Rescue (BDMLR) said.
At about midday on Tuesday, rescuers said the remaining whales had become stranded again and that it was assessing the situation.
One whale was refloated with the help of a police launch but said to be tilted to one side somewhat.
A BDMLR spokesperson said after the first whale was found dead: "Pilot whales sometimes strand when one is ill and it could be that the one found died and the others left on the rising tide."
Fifteen members of the rescue team had been planning to use specialist equipment to get across the mud and reach the whales. However, due to the inaccurate location reports, they could not find them on Monday.
Access on Monday evening was believed to be by Harty Ferry Road, with a walk of three-quarters of a mile (1.2km) across the mud.
Rescuers described the access conditions as "shocking".
Pontoons were being brought from London to help get 4x4 vehicles with equipment across the flats.
Members of the UK Cetacean Stranding's Investigation Programme, which handles all reports of stranded whales, will examine the site.
The organisation attends whale strandings so it can carry out post-mortems to determine whether they occurred naturally or have been driven by human activity.
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