Russia's Foreign Ministry on Thursday summoned the UK ambassador to "strongly protest" against what it said was a British destroyer's breach of its territory.
The dispute between Moscow and London erupted Wednesday after the HMS Defender passed near Crimea in the Black Sea.
Russia said it fired warning shots at the destroyer to ward it off. but Britain denied the claim.
Russia annexed Crimea from Ukraine in 2014 and claims the water around the peninsula as part of its territory.
Most countries including Britain did not recognise the takeover and stand behind Ukraine's claims to the water.
On Thursday, the Russian Foreign Ministry said it had summoned UK ambassador Deborah Bronnert and issued a "strong protest" over the British vessel's breach of Russian territory and its "provocative and dangerous actions".
"In the event of a repetition of such provocations, all responsibility for their possible consequences will rest entirely on the British side," the ministry said.
Kremlin spokesman Dmitry Peskov called the incident a "deliberate and prepared provocation".
The ministry said warning shots were fired and bombs dropped along HMS Defender's path before the ship left its territory.
Russia's FSB security services provided video of the warning shots that public TV channel Rossia 24 broadcast on Thursday evening.
In the film, Russian border guards repeatedly tell the British ship to change course and leave the area before the shots are fired.
"The Defender must not be hit," can be heard on the video, before the instruction, "Fire."
London said it believed Russia was conducting "a gunnery exercise" and had provided prior warning.
Incidents involving western aircraft and ships are not uncommon at Russia's borders, especially during heightened tension with Washington, Brussels and London, but rarely result in open fire.
Wednesday's incident comes before the Sea Breeze 2021 military manoeuvres to be held from June 28 to July 10 in the Black Sea.
The exercises will bring together more than 30 countries, including the US and Ukraine.