The "technology" of Moscow's oil refinery was not damaged in the overnight attack on Saturday, while three houses were damaged, said Moscow Mayor Sergei Sobyanin.
More than 120 drones had been downed in the previous 24 hours, he said.
Russia's defence ministry said 556 drones had been downed over the country, including the Moscow region, overnight and into the morning.
Moscow regional Governor Andrei Vorobyov posted on the Telegram messaging app that a woman had died when a home was hit in the city of Khimki, north of Moscow, while a rescue team was working to recover one person from the debris.
Two men died in the village of Pogorelki in the Mytishchi district, Vorobyov said.
One man was also killed as a drone struck a lorry in the Belgorod region.
Several high-rise residential houses and infrastructure facilities were also damaged.
Ukraine also attacked the Russian-occupied Black Sea peninsula of Crimea, damaging several apartment blocks in the capital Sevastopol, according to local authorities.
Debris from a downed drone struck a high-voltage power line, causing power cuts, Sevastopol Governor Mikhail Razvozhayev wrote on Telegram. However, the city's power station was not hit, he said.
A total of 25 drones were shot down over the city and the Black Sea, according to Razvozhayev.
It was not possible to independently verify the claims.
Meanwhile, Russia attacked Ukraine with 287 drones overnight on Sunday, 279 of which were shot down or jammed, the Ukrainian air force reported.
According to Ukraine's estate emergency service, the strikes injured 8 people in Ukraine's central Dnipropetrovsk region: three in the regional capital of Dnipro, four in Kryvyi Rih, and one in the district of Synelkove.
with dpa
