Mr Zelensky said attacks on Russian territory were an “inevitable, natural and absolutely fair process” of the war between the two countries.
Russia’s defence ministry said three Ukrainian drones were downed on Sunday, with two crashing into offices.
Vnukovo Airport, southwest of the city centre, was also briefly shut.
The drone attack in the early hours of Sunday is the latest that Moscow has blamed on Kyiv.
And in a video address on Sunday from the western Ukrainian city of Ivano-Frankivsk, Mr Zelensky said that Ukraine was getting stronger.
“Today is the 522nd day of the so-called ‘Special Military Operation’, which the Russian leadership thought would last a couple of weeks,” he said.
“Gradually, the war is returning to the territory of Russia – to its symbolic centres and military bases, and this is an inevitable, natural and absolutely fair process.”
This characterisation is certainly a level up from Kyiv’s normal approach of not admitting responsibility for attacks inside Russia.
It may be far from a confession, but President Zelensky clearly feels confident enough to pile on the pressure, and not just on the Kremlin.
Drone attacks like these are also an opportunity for him to address the Russian population, the majority of whom appear to believe Moscow’s invasion is just and righteous.
If they connect explosions close to home with what’s going on in Ukraine, as per Mr Zelensky’s suggestion, it makes it that bit harder for Vladimir Putin to justify his invasion, which he is only looking to expand.
Former Russian President Dmitry Medvedev said on Sunday that Moscow would have to use a nuclear weapon if Kyiv’s ongoing counter-offensive was a success.
Mr Medvedev, who is deputy chairman of Russia’s Security Council – a body chaired by Mr Putin – said on social media there would be “no other option” if Ukraine took what he described as “our land”.
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Officials said there were no injuries following Saturday’s drone attack, and the city’s mayor Sergei Sobyanin said the facades of two office buildings were slightly damaged.
Photos from the scene show that several windows have been damaged at the corner of the buildings, with debris scattered on the ground below.
One eyewitness, who only gave her first name as Liya, told Reuters news agency she could see fire and smoke.
“We heard an explosion and it was like a wave, everyone jumped,” she said.
“Then there was a lot of smoke and you couldn’t see anything. From above, you could see fire.”
Flights were briefly suspended from Vnukovo Airport, southwest of the city centre, and incoming planes were redirected to other airports.
In a statement, the defence ministry said the “attempted terrorist attack” had been “thwarted”.