The Ministry said two crew members on board the Su-34 fighter jet were able to eject as it crashed in a deserted area of the Voronezh region in Central Russia.
The Su-34, made by Russian aircraft manufacturer Sukhoi, first flew in 1990 but entered the Russian Air Force fleet in 2014.
In 2015, they were used during the Russian military intervention in Syria to attack ISIS targets. The estimated value is reportedly between $36m and $50m.
It was discovered in the Indiantown area of Williamsburg County, United States, according to officials. The search for the jet began on Sunday after its pilot was found on in North Charleston, South Carolina, after safely ejecting.
However, intercepted communications reveal that one of the Russian pilots believed he had been given permission to target the aircraft following an ambiguous command from a Russian ground station.
After firing, the first missile missed the RAF plane while the second failed to launch successfully. If it had reached its target, it could potentially have drawn a Nato member into a military confrontation with Mr Putin’s Russia.
The two Russian SU-27 fighter jets had encountered the RAF plane, which was carrying a crew of up to 30 people, as it was flying a surveillance mission over the Black Sea in international airspace on 29 September.