Russia has threatened to "drop bombs... right on target" if Royal Navy vessels sail again through waters around Crimea.
The Russian Defence Ministry has also released video of what it says shows HMS Defender 'violating' its border.
Russia claims a Su-24M warplane dropped four bombs close to Defender during an incident on Wednesday and alleged that a border patrol boat fired warning shots.
The British Government, which does not recognise Russia's claim to Crimea, denied the claims, with the Ministry of Defence (MOD) stating the Navy destroyer was conducting an "innocent passage" through Ukrainian waters.
Defence Secretary Ben Wallace has described the claims by Russia about the incident as "misinformation".
Russia's deputy foreign minister, Sergei Ryabkov, said "the inviolability of the Russian borders is an absolute imperative", adding that it will be protected "by all means, diplomatic, political and military if needed".
Asked what Russia would do if a similar incident happened again, he said: "We may appeal to reason and demand to respect international law.
"If it doesn't help, we may drop bombs and not just in the path but right on target if colleagues don't get it otherwise."
WATCH: Did Russia fire upon HMS Defender?
Mr Wallace said: "HMS Defender carried out a routine transit from Odessa 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 09:45 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.
"No shots were directed at HMS Defender and we do not recognise the claim that bombs were dropped in her path," the tweet added.
The earlier Russian statement claimed that Defender had "disregarded" a warning, before leaving the region, described as "the territorial sea of the Russian Federation".
Watch: Boris Johnson denies UK-Russian relations are at an 'historic low'.
Prime Minister Boris Johnson has echoed the statements made by the Government and the Defence Secretary, stating: "We don't recognise the Russian annexation of Crimea.
"These are Ukrainian waters and it was entirely right to use them to go from A to B," adding that HMS Defender had "proceeded in a way that you'd expect through international waters and in accordance with the law".
When asked if UK-Russian relations are now at "an historic low", Mr Johnson replied: "No, I can remember in my own lifetime when things have been far worse."
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.