A drone has hit a building in central Moscow that was under construction, Mayor Sergei Sobyanin has said.
Air defences also shot down two drones in the Mozhaisk and Khimki districts of the Moscow region, the defence ministry added.
There are no reports of casualties and it is not clear who carried out the attack.
Russian officials described it as "another attempt by the Kyiv regime to carry out a terrorist attack".
Ukraine does not usually comment on who is behind attacks inside Russian territory.
All flights were suspended to and from Moscow's airports early on Wednesday, a measure that has been taken repeatedly in recent days.
It was the sixth consecutive night of aerial attacks on Russia's capital region, AFP news agency reported.
The drone that hit the building under construction at the Moscow City complex had been suppressed by electronic warfare systems, the defence ministry said. It lost control and collided with the building, it added.
Several windows were smashed in two five-storey buildings opposite and emergency services were inspecting the area, the mayor added.
In response to reports of the downed drones, the US State Department said Washington did not encourage drone attacks in Russia.
US officials added it was up to Ukraine to decide how to defend itself, and that Russia could end the war at any time by withdrawing from its neighbour.
Also overnight, three elderly people were killed in Russian shelling near the eastern Ukrainian city of Lyman, officials said.
Allegations of drone strikes inside Russia have become increasingly common in recent months.
On Tuesday, Russia's defence ministry said it had downed two drones over the Moscow region, and two more were intercepted over the Bryansk region near the Ukrainian border.
Mr Sobyanin said Russian air defences had shot down two drones to the west of the capital in the Krasnogorsk and Chastsy districts. No injuries were reported.
The ministry also said a Russian warplane had destroyed a Ukrainian reconnaissance boat in the Black Sea that sailed near Russian gas production facilities on Tuesday.
Ukraine did not claim responsibility any drone incursions on Tuesday - but President Volodymyr Zelensky has previously said that attacks on Russian territory are an "inevitable, natural and absolutely fair process".
Source: BBC