Since the start of the war nearly a year ago, children as young as four months have been taken to 43 camps across Russia, including in Moscow-annexed Crimea and Siberia, for "pro-Russia patriotic and military-related education," said the report by the Yale Humanitarian Research Lab that was funded by the US State Department.
Nathaniel Raymond, a Yale researcher, said that Russia was in "clear violation" of the Fourth Geneva Convention on the treatment of civilians during war and called the report a "gigantic Amber alert" - referring to US public notices of child abductions.
The Russian activity "in some cases may constitute a war crime and a crime against humanity," he told reporters.
The report called for a neutral body to be granted access to the camps and for Russia immediately to stop adoptions of Ukrainian children.
Ukraine's government recently said that more than 14,700 children have been deported to Russia where some have been sexually exploited.
The US report, which relied on satellite imagery and public accounts, said that at least 6,000 children have been sent to camps but that the number is "likely significantly higher."
Russia has cast the effort as saving orphans or bringing children for medical care. Some parents were pressured to give consent to send away their children, sometimes with hopes they would return, the report said.
It said that Russian authorities have sought to provide a pro-Moscow viewpoint to children through school curricula as well as through field trips to patriotic sites and talks from veterans.
Children have also been given training in firearms, although Raymond said there was no evidence they were being sent back to fight.
The study said that Putin aides have been closely involved in the operation, especially Maria Lvova-Belova, the presidential commissioner for children's rights.
It quoted her as saying that 350 children have been adopted by Russian families and that more than 1,000 were awaiting adoption.