British Divers Marine Life Rescue said 18 of the animals were floated back out to sea at about 04:00 on Tuesday. Two more were later floated.
However, several of the whales then stranded on the shores of nearby Staffin Island.
It was understood that eight of the whales have died and nine remain stranded on the small island.
The coastguard said it could be high tide at 19:00 before those animals could be pushed back into open water.
It was believed the stranding was caused by a female whale getting into difficulty while calving. The calf died.
Hebridean Whale and Dolphin Trust raised the alarm after seeing whales in distress on Monday afternoon.
Environment Secretary Richard Lochhead said the Scottish government was offering assistance to the effort to save the whales.
He said: "I am very concerned to hear about this stranding of pilot whales on Skye.
"Marine Scotland and British Divers Marine Life Rescue are currently working hard to alleviate the situation.
"We have a patrol vessel and other staff on-site and I am being kept informed of the situation.
"Sadly it appears that some of the whales have already died and the situation is becoming increasingly difficult as the outgoing tide is leaving the stranded animals out of the water."
Rescuers have gone to the aid of 21 long-finned pilot whales which stranded on the shore at Staffin on Skye.