He said this during an informal meeting of the Security Council.
According to him, after the informal meeting of the Security Council in April, the Russian side received appeals in connection with the removal of children who are in European countries with their parents.
Nebenzia added that Russia is aware of dozens of such cases.
The diplomat noted that Ukrainian refugees do not know who to contact on such issues.
He also said that signals were also received from residents of EU countries.
"All this suggests that this problem is very serious and widespread," RIA Novosti quoted the permanent representative as saying.
Earlier, Russia's First Deputy Permanent Representative to the UN, Dmitry Polyansky, announced a meeting of the Security Council of the world organization on November 10 on the protection of Ukrainian children in the EU.