The northern bottle-nosed whale, the first sighted in the river since 1913, was in the water close to London's Albert Bridge. On Friday it had flailed through the murky waters of the Thames past Big Ben and the Houses of Parliament, watched by hundreds of curious onlookers.
Earlier Saturday a team of officials, including veterinarians and marine rescue experts, waded into the river to secure the whale with inflatable pontoons. A medical assessment was made, while experts decided how to continue with the operation.
A massive salvage vessel, the Crossness, was later brought to the scene. The was tethered to a sling and lifted aboard by a crane. The barge then headed east toward the North Sea.
However, a decision on whether the whale would be released or destroyed had yet to be taken as crucial medical assessments continued.
"This does not mean it is going to be released. Should the veterinary results be positive it would be released," said Tony Woodley, spokesman for the British Divers Marine Life Rescue group who are leading the rescue attempt.
Woodley had earlier described the whale's condition as "moderate."
The story of the whale has gripped Londoners, with many of them flocking to the banks of the river in west London to catch a glimpse of the massive mammal. London police were forced earlier on Saturday to clear the shore area of onlookers, as the whale prepared to beach.
Police estimated the crowd watching the operation numbered 2,000-3,000, and were forced to close a nearby bridge as numbers swelled.
"The guys out there are the best there we've got. But they have to make the hardest decision in the world now: Whether it's safe to move it or take the most humane option, which is euthanasia," said Laila Sadler, scientific officer at the Royal Society for the Prevention of Cruelty to Animals.
"We need to know how sick it is. If it was a healthy animal it can be moved. It has been done before many times. But it is already really stressed and really sick."
The whale, an adolescent male about 20 feet long, is normally seen in the deep northern Atlantic, diving deeply and traveling in pods. They can reach lengths of 26 feet, the size of a traditional red double-decker London bus.
When sick, old or injured, whales often get disoriented and swim off from their pod, said Mark Simmonds, science director at the Whale and Dolphin Conservation Society, although witnesses reported seeing a second whale in a different section of the river Friday.
Last week marine officials said they saw two bottle-nosed whales in northeastern Scotland when the mammals are normally seen in northwestern Scotland. That, coupled with the second sighting Friday, could suggest that something is disrupting the whales, Sadler said.
Scientists have said fluctuating ocean temperatures, predators, lack of food and even sonar from ships can send whales into waters that are dangerous for the mammals.