The Soviet star crowning the Stalin-era skyscraper, located just a kilometre from the Kremlin, was also painted in the yellow and blue colours of the national flag.
"The flag was attached by unidentified criminals to the top of the Kotelnicheskaya Embankment skyscraper," a spokesman for the Russian emergencies ministry, Roman Kilkeyev, told AFP.
Workers were brought in to remove the flag and give a new coat of gold-coloured paint to the star atop the 176-metre high building.
Moscow annexed Crimea from Ukraine in March, and a pro-Russian rebellion broke out in the east of the country that has led to some 2,200 deaths since April.