In a rare occasion of what appears to be the government bowing to public pressure, the plan was shelved Wednesday.
The St. Petersburg governor's office said the hospital would continue to treat patients and insisted there was no plan to change its location or profile when the Supreme Court and other top courts are relocated to Russia's second largest city after Moscow.
The Kremlin's property department also issued assurances that the hospital, on prestigious Krestovsky Island, would not be given over to judges of the top courts.
Even so, about 1,500 people took part in a planned evening protest, with some saying they did not trust officials to keep their word. Braving a bitter winter wind, they held up signs that said: "Children are more important than bureaucrats" and "You want to kill the hospital, but you will kill children instead."
"Even a one-day break in the work of the hospital is a potential murder," said protester Anna Ivanova, 29, a pediatrician who trained with the hospital's doctors.
"I'm sure that it is only the fact that people have come out to defend the hospital that it might be saved," said Nadezhda Dankova, 32, a pediatric nurse.
Yelena Grachyova, coordinator of a charity foundation that helps children and adults suffering from cancer, said the timing of the government's about-face was clearly aimed at thwarting the protest rally, which organizers had hoped would attract thousands. Grachyova said there had been previous attempts to take over the hospital because of the prime real estate it occupies, and she called for legal guarantees protecting it and other hospitals and schools on city property.
Putin has not weighed in on the hospital controversy.