Uefa has banned clubs in the annexed Crimea region from playing in competitions in Russia.
Two clubs moved from Ukraine's top division to Russia's third tier this season and played in the Russian Cup.
Ukraine Football Federation president Anatoly Konkov, sent a letter of complaint to Fifa and Uefa asking them to punish the Russian Football Union.
Uefa general secretary Gianni Infantino said Crimea would be designated a "special zone for football purposes".
The Russian annexation of Crimea is not recognised by the international community and the statutes of football's European governing body Uefa and world governing body Fifa prohibit clubs switching federations without consent.
Infantino said: "Having discussed this with the Ukraine and Russia, and Ukrainian and Russian football authorities, the executive committee came to the conclusion that for the time being the decision has to be to consider Crimea as a special zone for football purposes."
According to Russian third division rules, only players with Russian citizenship can take part in the league.
The decision affects three clubs in all - TSK Simferopol, SKChF Sevastopol and Zhemchuzhina Yalta.