Russian media reported a Russian border patrol boat fired shots at HMS Defender after the ship entered the country's territorial waters in the Black Sea.
The reports also claimed that a Russian jet dropped bombs near the Navy ship.
But the MoD has said the Royal Navy vessel was "conducting innocent passage through Ukrainian territorial waters in accordance with international law".
In a statement posted on Twitter, it said: "We believe the Russians were undertaking a gunnery exercise in the Black Sea and provided the maritime community with prior warning of their activity.
"No shots were directed at HMS Defender and we do not recognise the claim that bombs were dropped in her path."
Russian news agency Interfax reported earlier that Russian’s defence ministry said: "The destroyer was warned in advance that weapons would be fired in case of a violation of the Russian state border. It disregarded the warning.
"As a result of joint actions of the Black Sea Fleet and the Border Service of the Russian Federal Security Service, HMS Defender left the territorial sea of the Russian Federation at 12.23pm."
In a statement on Twitter, Ukraine's foreign minister Dmytro Kuleba said the incident showed that Russia's "aggressive and provocative policies" in the Black Sea and nearby Azov Sea constituted a "continuous threat to Ukraine and its allies".
He added: “We need a new quality of cooperation between Ukraine and NATO allies in the Black Sea.”
It is understood the two vessels met near Cape Fiolent, in the north of the Black Sea, on the coast of Crimea.
Russia seized and annexed the Crimea peninsula from Ukraine in 2014 and considers areas around the peninsula's coast to be Russian waters.
The move, however, has been condemned by the West, which believes the territory in question belongs to the Ukraine.
HMS Defender is part of the UK Carrier Strike Group currently heading to the Indo-Pacific region, but it is currently carrying out its own missions in the Black Sea.