An AFP reporter heard at least three loud explosions in the center of Kiev around 5:00 am (0200 GMT).
Sergei Popko, head of the Kiev City Military Administration, wrote on Telegram that two people were killed by falling debris.
Another person was injured and is being given medical aid, he said.
The military administration of the city of Kiev said the Russian military had launched groups of Iranian-made martyr drones and missiles from aircraft into the capital from different directions.
Earlier, Moscow’s Defense Ministry said a Russian plane “destroyed four high-speed military boats” in the Black Sea around midnight Moscow time (2100 GMT Tuesday).
The boats were “carrying landing groups of Ukrainian special operations forces, the total number of which was up to 50 people,” the ministry said in a telegram.
It did not specify where in the Black Sea the incident took place.
Early Wednesday, Russian security also foiled a “maritime drone attack” near the Sevastopol Bay in Crimea, local Moscow-based governor Mikhail Razvozayev was quoted as saying by the state-run TASS news agency.