Russia and Ukraine have hit each other's cities with barrages of drones during the conflict, now bogged down as Ukraine's troops fight a grinding counteroffensive.
The latest assault on Moscow comes hours after Ukrainian authorities said Russian artillery hit two villages near the eastern Ukraine city of Lyman, killing three people and wounding two others.
The Moscow region, hundreds of kilometres from the front line, has been repeatedly targeted in recent weeks, although there have been no reports of major damage.
Air defences downed one Ukrainian drone in Mozhaisky district and one in Khimki district of Moscow region, Russia's defence ministry said in a statement.
A third drone crashed into a building in the Moscow City business district around five kilometres (three miles) from the Kremlin after being "suppressed" by air defences, it said.
Air traffic at Moscow's Vnukovo, Sheremetyevo and Domodedovo airports was briefly halted, the TASS state news agency reported, citing the aviation services.
Footage posted to Telegram by Russian daily newspaper Izvestia showed a fire truck and other emergency services vehicles lined up along a street below a cluster of brightly-lit skyscrapers.
One window on a multi-storey building appeared to be damaged.
Emergency services were inspecting the area in the business district, Moscow mayor Sergei Sobyanin said on Telegram.
"Several windows were smashed in two adjacent five-storey buildings," he said.
Sobyanin and the defence ministry said there were no reports of casualties.
The RIA Novosti news agency reported an "explosion" was heard in the business district.
"A little later, smoke rose from the buildings in the same area," it said.
In recent weeks two other drone attacks were repelled over Moscow's financial district, each causing minor damage to the facades of high-rise buildings.
In May, drones were shot down near the Kremlin.
- Air and sea -
Russia and Ukraine have also ramped up attacks in the Black Sea since the July collapse of a UN-brokered deal which aimed to ensure safe navigation for civilian grain shipments from Ukraine ports.
Moscow said on Tuesday it had destroyed two Ukrainian military boats in the strategic waterway, including one carrying troops.
Russia also said that it dispatched two fighter jets to intercept two drones over the Black Sea, without specifying which country had deployed them.
The incidents came after the first civilian cargo ship sailing through the Black Sea from Ukraine recently arrived in Istanbul in defiance of the Russian blockade.
Since exiting the deal Moscow has pounded Ukraine's southern Odesa and Mykolaiv regions that are home to ports and infrastructure vital for shipment of grain.
Kyiv has attacked Russian ships in its waters and the Crimean Peninsula, which was annexed by Moscow in 2014.
Early on Wednesday Ukrainian authorities issued an air warning for the Odesa region, according to the head of the local administration.
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