Crimean clubs have been suspended by UEFA from playing in Russian domestic competitions.
"The Russian Football Union (RFU) may not organise any football competition in Crimea, without the consent of UEFA and the Football Federation of Ukraine (FFU)," it said in a statement on Thursday, adding the ban would take effect on Jan. 1.
Gianni Infantino, secretary general of European soccer's ruling body, added that UEFA would fund development projects in the region in the meantime.
"This solution brings the situation into line with the statues of UEFA and FIFA and ensures football can be played and developed in Crimea," he told reporters.
"It is not up to UEFA to determine any political situation, it is about football. The UEFA executive committee is interested that football can be played."
The RFU has included three Crimean clubs in the southern zone of its second division, the country's third tier, after renaming them TSK Simferopol, SKChF Sevastopol and Zhemchuzhina Yalta.
According to the regulations of world soccer's governing body FIFA, football leagues or clubs may only be affiliated by other associations and play on their territory in exceptional situations and with the consent of all sides.
Ukraine says Russia has no right to include the Crimean clubs in its leagues as the peninsula is officially regarded as an occupied territory and its separation has not been globally recognised.
Russia annexed the Crimean peninsula in March soon after Ukrainian protesters toppled pro-Moscow President Viktor Yanukovich.
Infantino said a disciplinary case could be opened if UEFA's decision was not respected.