Speaking on the sidelines of the United Nations General Assembly, Olena Zelenska said more than 19,000 Ukrainian children have been taken to Russia or occupied territories since the war began.
So far, only 386 have been brought back, the AFP news agency reported.
Ms Zelenska said that in Russia, the children were being told “that their parents don’t need them, that their country doesn’t need them, that nobody is waiting for them.”
“The abducted children were told that they are no longer Ukrainian children, that they are Russian children,” she said.
The call comes after a group of 48 children from Ukraine arrived in Belarus on Tuesday from regions Moscow claims to have annexed.
The children came from towns captured by the Russian army in July 2022, as well as the occupied Donetsk, Luhansk and Zaporizhzhia regions.
The removal of the children from Ukraine was organised by a Belarusian charity, supported by the country’s president, Alexander Lukashenko.
Belarusian officials have denied allegations that Belarus has helped to remove children illegally from Ukraine.
In June, Belarusian opposition figures gave the International Criminal Court materials which they said showed more than 2,100 Ukrainian children from at least 15 Russian-occupied Ukrainian cities who were forcibly removed to Belarus with Mr Lukashenko’s approval.
Pavel Latushka, a former minister, said he hoped the material would prompt the ICC to issue an arrest warrant for Mr Lukashenko, as it did with Russian President Vladimir Putin.
“We are seeing more and more evidence relating to the illegal transfer of Ukrainian children to Belarus and this will continue until international organisations react and stop Minsk," Mr Latushka.
In March, the ICC issued arrest warrants for Putin and Russia’s children’s rights commissioner, Maria Lvova-Belova.
Judges in The Hague, Netherlands, said they found “reasonable grounds to believe" the two were responsible for war crimes, including the illegal deportation and transfer of children from occupied Ukrainian regions to Russia.
Belarus has been Moscow’s closest ally since the Russian invasion began in February 2022, when Mr Lukashenko allowed the Kremlin to send troops and weapons into Ukraine from Belarus.