The whales were found on the Lincolnshire coast over the weekend - two at Gibraltar Point and another in nearby Skegness.
Jan Smith, who led a team of 14 workers to remove the 30-tonne animals, said it had gone more smoothly than expected.
The work took place at night to keep disturbance to a minimum, he said.
Mr Smith said he expected the "delicate operation" to take up to eight hours, but all were removed by 01:30 GMT. The process started just after 20:00 in Skegness.
"It's gone very well, really," he said.
"The last one where the flaps had been cut open for the autopsy was hard work.
"You can't really plan what you are going to do because you don't know if they are likely to blow up or something. All that you can do is treat them with the utmost respect.
"It's a delicate operation."
The whales were positioned on to three low-loaders before being taken away. They will be buried in a landfill site in Sheffield.
The public were being warned to keep their distance while the work took place because of safety concerns.
The warning came after one of the whales "decompressed rather spectacularly" while scientists were carrying out tests on it.
Hundreds of people have turned out to see the mammals since they were discovered.
Footage has emerged showing what could be two of the whales swimming in the North Sea on Saturday.
Two other whales washed up on the east coast - one is on the site of a former bombing range near Wainfleet in Lincolnshire. Another was found in Norfolk on Friday.
The carcasses of three sperm whales washed up on the east coast have been taken to landfill sites in an overnight operation.