RIA Novosti, a Russian state news agency, played up the incident as a victory for Russia, running with the headline: "Navy and air force expel North Atlantic Treaty Organisation destroyer violating border in Black Sea".
However, the UK's defense ministry swiftly denied the incident's occurrence.
London said it believed Russian Federation was "undertaking a gunnery exercise" and had provided prior warning of its activity.
The HMS Defender left Russian waters soon after the incident, having ventured as much as 3 kilometres (2 miles) inside, the Russian ministry said, adding that the confrontation took place near Cape Fiolent, a landmark on the coast of Crimea.
Moscow said the three Ukrainian ships made an unauthorized passage through Russian territorial waters, while the Ukrainian government insisted that its vessels were simply moving towards the narrow Kerch Strait which separates the Crimean peninsula from the Russian mainland that Russia had blocked.More news: Canada is lifting some major travel restrictions for fully-vaccinated residents
On Wednesday, UK Defence Secretary Ben Wallace said in a statement that the HMS Defender had been carrying out a "routine transit from Odesa towards Georgia across the Black Sea".
A Russian jet also dropped bombs in its path as a warning, the ministry said.
"As is normal for this route, she entered an internationally recognised traffic separation corridor", Wallace said in a public statement.
"She exited that corridor safely at 0945 BST (6.45pm AEST)".
"As is routine, Russian vessels shadowed her passage and she was made aware of training exercises in her wider vicinity", he added.
HMS Defender is a Type 45 destroyer that is part of the UK's Carrier Strike Group and is now heading towards the Indo-Pacific region.More news: Court turns back European Union demand for surge in AstraZeneca vaccine doses
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.
"Naturally, we can not but be concerned over the continuous buildup of North Atlantic Treaty Organisation military potential and infrastructure near Russian borders, as well as the fact that the Alliance is refusing to consider constructively our proposals on de-escalating the tension and reducing the risk of unpredictable incidents", Putin told a Moscow conference on worldwide security. "HMS Defender was going to sail within the 12-mile limit of Crimea's territorial waters", Beale reported.
Ukraine is struggling to rebuild its naval forces. Under the deal - which was also co-signed by United Kingdom defence company Babcock and paid for by loans from the British government - the United Kingdom will help build new naval bases for Ukraine and sell Ukraine two refurbished small warships.
Sergei Tsekov, a senator for the legislature of Crimea, called the British warship's movements "a flagrant violation of global norms and standards", warning that it could "provoke a serious conflict", according to state media.
Russia's embassy in Washington late Tuesday night expressed concern about ongoing North Atlantic Treaty Organisation drills in the Black Sea. We presume that it is a military organisation.More news: US CDC classifies Delta variant as ‘variant of concern’