The Soviet star on the Stalin-era skyscraper 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 Kotelniki skyscraper", a spokesperson for the Russian emergencies ministry, Roman Kilkeyev, told AFP.
Workers were brought in to remove the flag and give the star a new coat of gold-coloured paint.
Tensions between Moscow and Kiev have soared since Viktor Yanukovich was chased from power in Ukraine and replaced with a pro-Western government in February.
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.