UK prime minister Boris Johnson has stood by the decision to sail a warship through Black Sea waters claimed by Russia after Moscow threatened it would bomb British ships in the event of further “provocative steps” in the region.

The dispute was sparked on Wednesday when Russia said it had fired warning shots and dropped bombs in the path of HMS Defender, a British destroyer, as it sailed through contested waters off the coast Crimea on its way from Ukraine to Georgia. The UK’s Ministry of Defence denied that its ship had been fired at and said the shots had been part of a Russian “gunnery exercise”.

In Moscow, UK ambassador Deborah Bronnert was summoned and issued with a “decisive protest” over the incident, Russia’s foreign ministry said on Thursday. “It was particularly emphasised that in the case any such provocations are repeated, all responsibility for any possible consequences will lie entirely with the British side.”

When questioned about the warship’s deployment, the British prime minister refused to say whether he had personally approved the destroyer’s route through disputed waters, which Russia has claimed since its annexation of Crimea from Ukraine seven years ago. But Johnson made clear that the mission was a gesture of solidarity with Kyiv.

“The important point is that we don’t recognise the Russian annexation of Crimea, this is part of a sovereign Ukrainian territory,” he told reporters on Thursday. “It was entirely right that we should vindicate the law and pursue freedom of navigation in the way that we did, take the shortest route between two points, and that’s what we did.”

HMS Defender, which is accompanying the UK’s HMS Queen Elizabeth aircraft carrier on a long-planned deployment to the Indo-Pacific, had split from the rest of the battle group for a port stop in Odesa where British and Ukrainian officials signed a new defence agreement.

Warning against any further British action in the region, Russia’s deputy foreign minister Sergei Ryabkov said Moscow would fire on British ships if they took “provocative steps” to challenge its claims to waters and would use “diplomatic, political, and, if necessary, military means” to defend its borders.

“We can appeal to reason and demand respect for international law. If that doesn’t help, we can drop bombs not just in the path, but right on target, if our colleagues don’t get it,” Ryabkov told reporters, according to state-owned newswire Tass.

“The territorial integrity of the Russian Federation is inviolable. The integrity of its borders is an absolute imperative,” he said. “Those who try to test our mettle are taking high risks.”

Russia said it sent a coastguard ship to fire warning shots, then deployed an attack plane to drop high explosive fragmentation bombs in the path of HMS Defender after it ignored orders to change course.

UK defence secretary Ben Wallace presented a different version of events. At 9.50am British time, HMS Defender conducted “innocent passage through Ukrainian territorial waters” via a traffic separation scheme, he said in a written statement to parliament.

But 10 minutes later, a Russian coastguard vessel warned that Russian units would shortly commence a “live fire gunnery exercise”, according to the statement. Artillery was detected at 10.08am behind the warship, but this was “out of range of her position” and “posed no danger” to the British vessel, according to the defence secretary.

He added that HMS defender had been overflown by Russian combat aircraft at varying heights, the lowest of which was approximately 500 feet. “These aircraft posed no immediate threat . . . but some of these manoeuvres were neither safe nor professional,” Wallace’s statement read.