The move will be seen by some as a publicity stunt to boost the president's popularity amid falling approval ratings.
The whales have been held in enclosures in far eastern Russia since last summer by commercial firms that planned to deliver them to aquariums, including in China where the industry is booming.
Scientists and celebrities had called for their release.
On Thursday, a state television journalist reported live from a gangway beside the enclosures near the far eastern port town of Nakhodka after eight were taken away to be released in their native habitat in what she hailed as a "miraculous effect of the phone-in".
There has been a debate over whether to release the whales directly from the pens off the port of Nakhodka or, in a much more costly process, return them to the Sea of Okhotsk where they were caught -- more than 1,300 kilometres (800 miles) to the north.
Russian officials said the eight whales, and others still in captivity, would all be freed in the Sea of Okhotosk.
"Right now two killer whales and six belugas are being taken to the Shantar Islands to finally set them free," the TV reporter said.
The feel-good resolution to the controversy was reached during Putin's phone-in, where he often resolves ordinary people's problems on the spot and upbraids officials.
Putin, who has previously taken part in tagging an endangered beluga whale to help conservation research, said that the issue had been the animals' high commercial value.
"The killer whales alone -- as far as I know -- are worth around 100 million dollars... When it's big money, problems are always hard to solve," Putin said.
"Thank God things have started moving."
Russian television filmed a container with whales being loaded onto a truck with a crane early in the morning on Thursday.
The whales will travel partly by boat along the Amur River, a television reporter said.
Deputy prime minister Alexei Gordeyev told Putin live on air that the government would change the law to ban hunting whales for "educational and cultural purposes" - a loophole used to capture these whales.
He said that the "right decision was taken on the recommendation of scientists" to release the mammals in their native habitat.
It will take "around four months" to release all the whales in the groups that they have been living in, he said.
The companies that caught the whales have been fined.