Russia summoned the British ambassador and accused the UK of staging a “crude British provocation” on Wednesday after a Royal Navy warship sailed through Black Sea waters off the coast of Crimea.

The Russian defence ministry claimed it fired warning shots to chase away HMS Defender after it ignored several warnings and made a 3km incursion near Cape Fiolent on the southern tip of the contested peninsula, which Russia claims.

But the UK’s Ministry of Defence denied that any shots were fired directly at the vessel, saying the Russians had given prior warning that they were “undertaking a gunnery exercise” in the area.

Russian state media published videos of planes buzzing HMS Defender but did not show any videos of the supposed warning shots.

Ben Wallace, UK defence secretary, said HMS Defender was on a “routine transit” from Odessa to Georgia across the Black Sea. But the incident appears to have been part of a UK attempt to show support for Ukraine, which lost Crimea when Russia annexed it in 2014.

Though most countries do not recognise Moscow’s control of Crimea, Russia’s Black Sea fleet has repeatedly denounced similar visits by warships from members of Nato, which Ukraine recently made an unsuccessful push to join.

“As is normal for this route, [the destroyer] 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,” Wallace said.

Wallace later compared the incident to Moscow’s claims in May that its navy and air force had chased another UK destroyer, HMS Dragon, out of waters near Crimea last autumn — a statement he described as “factually untrue”.

“These are the things that come and go with Russia . . . disinformation is something we have seen regularly, we’re not surprised by it, we plan for it, and we take all steps to make sure we are not escalatory or indeed provocative,” the defence secretary told MPs. “However, we will not shy away from upholding international law and our rights on the sea.”

The Russian defence ministry said that, after HMS Defender did not respond to repeated warnings from Russian forces that they would open fire, a coastguard ship fired warning shots at it.

Minutes later, Russia’s Black Sea Fleet scrambled a Su-24M attack aircraft that dropped four high-explosive fragmentation bombs in the ship’s path before it exited the waters, according to the ministry.

Tom Sharpe, a retired Royal Navy commander, said the UK was not breaking any laws by conducting a freedom of navigation exercise in the area.

“Can warships transit through other countries’ waters without permission? Absolutely — international law permits it,” he said, adding that the UK would be “learning lessons” from this interaction ahead of the HMS Queen Elizabeth aircraft carrier’s planned passage through the South China Sea later this year.

Mark Galeotti, a senior associate fellow at the Royal United Services Institute, said Moscow “was trying to show it’s not going to be pushed around” by “provocative” actions such as HMS Defender’s voyage.

“The Brits are often in this role as a proxy — they [the Russians] don’t want to be too aggressive against the Americans [ . . . ] so there is a sense you do it against the Brits because it’s not quite as dangerous,” he said.

The disputed claims come at a time of heightened tensions between Russia and the Nato alliance.

Earlier on Wednesday, president Vladimir Putin told a defence conference in Moscow that Russia “could not fail to be concerned by Nato’s ceaseless ramping up of its military potential near Russia’s borders as well as the alliance’s refusal to constructively consider our suggestions to de-escalate tensions and reduce the risks of unpredictable incidents.”

HMS Defender, which forms part of the UK’s carrier strike group deployment, visited Odessa this week in a show of support for Ukraine’s territorial integrity. British and Ukrainian officials met on board the destroyer on Tuesday to agree a defence deal in which the UK will help boost Kyiv’s naval capabilities.

The co-operation will include training of Ukrainian navy personnel, the creation of new naval bases, and the purchase of two Sandown class minehunters.