The Iskanders are also reported to be protected by long-range air defence and coastal defence missiles at the Chernyakhovsk military base.
Greg Bagwell, a retired air marshal and former deputy commander for RAF operations, labelled the deployment of Iskanders as a “provocation”
He said: “When someone brings out new kit you always want to go and have a look at it.”
The jets were flown from RAF Waddington in Lincolnshire and also carry a radar that can pinpoint the where military units are located on the ground.
The planes are tasked with spying on on Iskander missiles deployed, according to defence sources.
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The news has come after RAF Typhoon fighter jets were scrambled to intercept Russian planes as they approached UK airspace earlier this year.
The Ministry of Defence released footage of the two British jets flying alongside the Russian bombers – known as Blackjacks by NATO.
Russia claimed the incident and reaction was designed to make the superpower look “aggressive” and criticised the Prime Minister for “showing off”.
It came just weeks after British warship HMS Westminster intercepted a Russian vessel in the English Channel on January 8.
NATO and Russia remain at loggerheads over accusations from both sides about military build-up in Eastern Europe.
Both sides claim the other is using the excuse of defence to send tanks, soldiers and missiles into the fragile region.
Earlier this month, hundreds of British soldiers were deployed to Estonia to take part in ultra-realistic war games and offer military deterrence against Russia.
The deployment of troops was a bid to deter Russian aggression and prove Nato is a “very capable force” ready to deal with a raft of threats, a senior UK officer said.
Britain has also attacked Putin for allegedly spreading “fake news” and attempting to interfere in elections.