The Ministry of Defence (MOD) has denied that a Royal Navy vessel was subjected to warning shots being fired.
The Russian Defence Ministry claimed a border patrol boat fired warning shots at HMS Defender and a Su-24M warplane dropped four bombs close to the ship, in a statement reported by the Russian Interfax news agency.
The UK has, however, stated those claims are untrue.
The Defence Secretary Ben Wallace said: "HMS Defender carried out a routine transit from Odesa towards Georgia across the Black Sea.
"As is normal for this route, she entered an internationally recognised traffic separation corridor. She exited that corridor safely at 0945 BST.
"As is routine, Russian vessels shadowed her passage and she was made aware of training exercises in her wider vicinity."
"No warning shots have been fired at HMS Defender," the MOD Press Office tweeted.
"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.— Ministry of Defence Press Office (@DefenceHQPress) June 23, 2021
No shots were directed at HMS Defender and we do not recognise the claim that bombs were dropped in her path.
"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."
The earlier Russian statement claimed that Defender had "disregarded" a warning, before leaving the region, described as "the territorial sea of the Russian Federation".
The UK does not recognise Russia’s claim to Crimea.
Watch: Ben Wallace addresses Russian 'misinformation' about HMS Defender.
HMS Defender, a Type 45 destroyer, is currently on the UK's maiden operational Carrier Strike Group 21 deployment, and is "one of the most advanced warships ever constructed", according to the Royal Navy.
It was announced earlier this month that she would be temporarily breaking away from the deployment to carry out her "own set of missions" in the Black Sea.
Yesterday, the destroyer's official Twitter account posted an update stating she was leaving the Ukrainian city of Odessa "to continue our operations in the Black Sea".
The Russian Embassy in the UK this afternoon accused HMS Defender of violating the Russian border, dubbing it "HMS Provocateur".
HMS Defender turns HMS Provocateur and violates Russian border. Not exactly a "routine" transit, is it? https://t.co/yetauFlF6opic.twitter.com/GnMkSJFP8s— Russian Embassy, UK (@RussianEmbassy) June 23, 2021
During a NATO summit in Brussels last week, the alliance's Secretary General described relations with Russia as being at "its lowest point since the end of the Cold War".
US President Joe Biden also called on Russia to cease provocative actions against NATO members.
This week, the UK signed a defence deal with Ukraine on board HMS Defender, including an agreement to help build naval bases around the Azov Sea and the Black Sea regions.