The Russian capital’s Domodedovo and Vnukovo airports are understood to have been temporarily closed.
All aircraft have been grounded, with neither also able to receive any flights.
Instead, planes are reportedly being redirected to Sheremetyevo – more than 50 miles away.
It comes after one of Vladimir Putin’s prized war planes was damaged after a kamikaze drone strike deep inside Russian territory on Saturday.
The attack, at the military airport in the Novgorod region more than 700 miles from Ukraine, witnessed a “helicopter style” drone.
The ministry said nobody was hurt and the fire was quickly extinguished.
The aircrafts which survived the attack are reportedly being being moved to an airfield in the Murmansk region.
The Russian defence ministry said: “The Kyiv regime carried out a terrorist attack using a copter-type UAV on a military airfield in Novgorod region.”
“As a result of the terrorist attack on the territory of the airfield, a fire broke out in the aircraft parking lot, which was promptly eliminated by fire brigades.
“One plane was damaged, but there were no casualties as a result of the terrorist attack.”
It also follows a huge explosion that rocked Moscow on Friday after a suspected Ukrainian kamikaze drone blasted a building just three miles from the Kremlin.
Footage showed flames and a column of black smoke rising from the Moscow Expocentre after the strike.
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