The alleged incident took place in October off the coast of Crimea but has only been made public now.
Moscow claimed that HMS Dragon ignored 'warnings' not to enter 'Russian territorial waters' and warplanes and ships were dispatched to move her along.
The Ministry of Defence has since fired back at the claims this week.
It comes ahead of the expected deployment of some of HMS Queen Elizabeth’s carrier strike group flotilla to the Black Sea as part of the aircraft carrier’s maiden mission to the Far East.
'HMS Dragon was taking the most direct route between two port visits, navigating a recognised safe route for all international shipping within Ukrainian waters,' a spokesman from the MoD told the Daily Mail.
'The Russian Federation Navy did not impede HMS Dragon’s passage. She navigated without incident, exercising our right of innocent passage under the UN Convention on the Law of the Sea,' he added.
In 2018, HMS Dragon’s sister ship, HMS Duncan, was swarmed by Russian jets during a deployment to the Black Sea.
It followed Russia’s controversial annexation of Crimea in 2014.
A documentary crew on Duncan filmed the moment 17 Russian warplanes flew over the £1bn British warship,