The Russia Defence Ministry said shots were fired and bombs were dropped in the path of HMS Defender in waters off Crimea.
A border patrol boat fired warning shots at HMS Defender and a Su-24M warplane dropped four bombs, the defence ministry said in a statement reported by the Russian Interfax news agency.
“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,” the statement said.
“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.”
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But in a statement posted on Twitter, the MoD said: “No warning shots have been fired at HMS Defender.
“The Royal Navy ship is conducting innocent passage through Ukrainian territorial waters in accordance with international law.
“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.”
HMS Defender – a Type 45 destroyer – is part of the UK Carrier Strike Group currently heading to the Indo-Pacific region.
However, it was announced earlier this month that it would be temporarily breaking away from the group to carry out its “own set of missions” in the Black Sea.
The reported incident took place off the coast of Crimea, which was annexed by Russia from Ukraine in 2014.
Tensions in the region have been running high for some months.
In April the United States scrapped plans to deploy two of its destroyers to the Black Sea amid concerns over a build-up of Russian forces on the Ukrainian border.