The strike targetted the Ukrainian Security Service command post, the state-run Kyiv design bureau "Luch," and positions of the Patriot anti-aircraft missile system, the Russian Defence Ministry said in a statement.
It said the raid was in response to Ukraine's Wednesday attack on a Russian chemical plant in the Rostov region with six US-made ATACMS tactical missiles and four Storm Shadow air-launched cruise missiles.
Ukraine's General Staff of the Armed Forces said on Telegram that five Russian missiles targeted Kyiv but were shot down by Ukrainian air defence at around 7 am (0500 GMT).
The fragments of downed missiles resulted in deaths and injuries as well as damage in five districts of Kyiv, it said, Xinhua news agency reported.
In a major shift of policy on the Ukraine crisis, the United States in November authorized Ukraine to use US long-range missiles to strike targets in Russia, triggering an escalation of tension around the conflict.
Earlier this week, citing a senior diplomat, the Ukrainian government-run Ukrinform news agency reported that Russia has carried out 12 attacks on Ukraine's energy infrastructure so far this year, launching about 1,100 missiles.
Sergiy Kyslytsya, Ukraine's Permanent Representative to the United Nations, said that the attacks involved both cruise and ballistic missiles.
Russia last week conducted one of the largest assaults this year on Ukraine's energy facilities with 94 missiles and 193 drones, Kyslytsya said.
Earlier, the state-run energy company Ukrenergo estimated that Ukraine had lost about nine gigawatts of generating capacity due to the strikes.
Later, the Russian authorities also detained an Uzbek citizen in connection with the deaths of a senior military official and his assistant.
The 29-year-old suspect has been accused of carrying out a terrorist attack that resulted in the deaths of Lieutenant General Igor Kirillov, head of the Russian armed forces' radiological, chemical and biological defence troops, and his assistant.
According to the Russian Investigative Committee, the suspect was recruited by Ukrainian intelligence services and given a homemade explosive device after he arrived in Moscow. He allegedly placed the device on an electric scooter parked near the entrance of the building where Kirillov resided.
int/as