"At 12:19 a Su-24M carried out a warning bombing run using 4 OFAB-250 [hihgh-explosive fragmentation] bombs at the HMS Defender's path of movement", the statement added.
The incident marked the first time since the Cold War that Moscow has used live ammunition to deter a North Atlantic Treaty Organisation warship, reflecting growing risks of military incidents amid soaring Russia-West tensions.
Defence Secretary Ben Wallace said in a statement that HMS Defender had been carrying out a "routine transit from Odesa towards Georgia across the Black Sea".
The Russian Defence Ministry said it had summoned the United Kingdom military attache in Moscow to protest the British destroyer's manoeuvre.
The Defence Ministry has concentrated special attention to ensuring the security of Crimea, with pro-Western authorities in Kiev and North Atlantic Treaty Organisation nations refusing to recognise Russian jurisdiction over the peninsula, notwithstanding a popular referendum which saw the overwhelming majority of the territory's residents vote to break off from Ukraine and rejoin Russia in early 2014 in the aftermath of the Maidan coup.
"As is normal for this route, she entered an internationally recognised traffic separation corridor".
That HMS Defender in the Black Sea to sell warships to Ukraine - against whom Russian Federation has been openly fighting and attempting colonisation regions of for years - may go some way to explain the hostility on Wednesday morning. Wallace echoed the Defence Ministry's claims that the British ship was informed of Russian "training exercises in her wider vicinity".
The MOD insisting HMS Defender was in Ukranian water may be seen as a tacit denial they ever entered Russian waters, as Moscow claimed.
The UK does not recognise Russia's claim to Crimea, in line with the worldwide consensus that Russia's annexation of Crimea is illegal.
Ukraine's Foreign Minister Dmytro Kuleba said the incident was "a clear proof of Ukraine's position: Russia's aggressive and provocative actions in the Black and Azov seas, its occupation and militarization of Crimea pose a lasting threat to Ukraine and allies".
Earlier in the day, Moscow urged the United States and its North Atlantic Treaty Organisation allies to stop military operations in the Black Sea region, calling instead for "multilateral efforts" aimed at maintaining stability, and for states in the region to resolve problems without unwanted "help" from outside powers.
The Royal Navy's Type 45 Destroyer, HMS Defender.
The Russian military began tracking the HMS Defender and the Royal Netherlands Navy's HNLMS Evertsen frigate on 14 June after the pair of North Atlantic Treaty Organisation warships entered the Black Sea.
"The moves by warships of the US and its allies have been clearly provocative", Gerasimov said at an global security conference in Moscow organized by the Defense Ministry.
Speaking on Wednesday just before the incident, General Valery Gerasimov, the chief of the general staff of the Russian armed forces, sharply criticised the deployments of North Atlantic Treaty Organisation warships near Russian waters.
He charged that the British destroyer Dragon intruded into the Russian waters near Crimea in October, and the US destroyer John McCain violated the Russian border in the Sea of Japan in November.
'The destroyer was warned in advance that weapons would be fired in case of a violation of the Russian state border.
Moscow withdrew some of its forces after sweeping manoeuvres but Ukrainian officials said the bulk of them remained.