Ten whales were successfully refloated and they made their way out of the harbour. However, officials suspect a whale found dead the following day further down the coast, near Leith in Edinburgh, was from the same group.
Experts voiced disappointment that the pod appeared to have headed south-west after being freed, rather than heading north to deeper waters.
Post-mortem examinations to try to determine what caused the whales to be stranded have been carried out by experts from the Scottish Agricultural College and the Zoological Society of London.
Fife Council began work on Monday to remove the carcasses of the animals that died on the region's coastline. The local authority's head of environmental services, Dr Bob McLellan, said the initial stage of that process is now over.
"All whales have now been removed from the shore to the top of the cliff where they are being stored," he said. "The vets and pathologists are finishing off their work before the carcasses are transported up north to the Moray area for disposal."