Another submarine, a Kilo-class vessel from the same fleet, is believed to have travelled through the English Channel after it was spotted by Norwegian ships when it surfaced further north.
The three ships were being closely watched by a Royal Navy submarine - which has Russian speaking technicians - and tracked them closely for six hours.
The Royal Navy submarine is due to be joined by another from Nato, which earlier this week advised Spain to refuse Russia's request to land its flotilla at a Spanish port on the African coast.
"In the South West approaches, the Russian submarines made it clear that they wanted us to know they were there. Then, after a period of time, they went deep. They were located once more with support from a Nato partner," said a naval source.
The recent sightings come just days after the Russian navy unveiled their new super-stealth submarine, which will be deployed in the Black Sea.
The Veliky Novgorod is the latest addition to the Black Sea fleet and is capable of striking land, sea and underwater targets.
The Kilo-class ships, one of which was thought to have been in the English Channel, is believed to be the quietest diesel-powered ship in the world.
Several Nato states, including Estonia, fear they could be next on President Putin's hit list. And fellow members, including the UK, have a legal duty to defend them.
The alliance's build-up will see 800 UK troops deployed to Estonia for six months from May. They will be relieved by soldiers from another Nato nation to keep up a continuous presence.
Sir Michael Fallon said the British mission would incorporate Challenger 2 tanks, Warrior vehicles and hand-held drones.
Speaking at Nato headquarters in Brussels, the Defence Secretary added: "This is Britain stepping up in Nato, beefing up the reassurance that we are able to offer.
"Although we are leaving the European Union, we will be doing more to help secure the eastern and southern flanks of Nato."
An MoD spokesman added: "The UK is stepping up its package of measures to support its allies in Europe, in the face of a more assertive Russia."
Tensions between Russia and the West have escalated due to Moscow's indiscriminate bombing of civilians in Aleppo.
President Putin sent a fleet of eight Russian warships through the English Channel to assist the assault on the besieged Syrian city.
But this week, following pressure from its Nato allies, Spain withdrew permission for the ships to refuel in Ceuta because Moscow was unable to pledge the vessels would not be used to bomb Syria.