A Russian “spy ship” was tracked closely by the Royal Navy this week after it entered UK waters on Monday and passed through the Channel at a time of heightened concern about the safety of undersea cables.

The defence secretary, John Healey, told the Commons on Tuesday that the Yantar, a Russian vessel engaged in “mapping the UK’s critical underwater infrastructure”, had passed through British waters for the second time in less than three months.

Healey accused the Russian president, Vladimir Putin, of trying to threaten European security by targeting undersea infrastructure carrying oil, gas, electricity and the internet. “We see you. We know what you’re doing,” he said before MPs.

The Yantar, officially an ocean research vessel, was first picked up 45 miles (70km) off the British coast, well inside the UK’s exclusive economic zone (EEZ) on Monday. “Let me be clear, this is a Russian spy ship,” Healey told MPs.

It had previously sailed through UK waters in November, when Healey said it had been “detected loitering over UK critical undersea infrastructure”. It then sailed into Irish waters east of Dublin, raising concern it was spying on internet connectors running between the UK and Ireland.

Healey said it had been tracked at the time by a submarine, warships and patrol aircraft. The submarine, thought to be HMS Astute, had been ordered to surface close to the Yantar “to make clear that we had been covertly monitoring its every move”, he said.

This time the vessel did not loiter and was followed by the frigate HMS Somerset and patrol ship HMS Tyne, which had been authorised to get closer to better track it, Healey said.

Cables under the Baltic Sea have been damaged in unclear circumstances three times in the past 18 months. An oil tanker dragging its anchor damaged a power cable running between Finland and Estonia on Christmas Day, prompting Nato allies to step up patrols of the region.

It is unclear who was responsible for the incident, which involved the Cook Islands-registered Eagle S, but Healey told MPs that “many analysts believe this was caused by a vessel in Russia’s shadow fleet”.

Britain and other Nato countries are anxious about threats to undersea infrastructure, which are often critical to a nation’s needs but are hard to defend. They believe the threat from Russia has stepped up since its invasion of Ukraine, with Moscow considering itself involved in a conflict with the west.

Katja Bego, a research fellow at the Chatham House thinktank, said that undersea cables are vulnerable to “deliberate weaponisation”. Though there is enough backup to ensure severing one or two cables won’t lead to a loss of a service, she added, “these networks would find it harder to withstand an attack in which many cables were damaged at the same time”.

Though Healey’s description of the Yantar as a spy ship did not come as a surprise to experts, it did show that the UK remains willing to call out Russian espionage activity, which is at times brazen but not always publicly acknowledged.

The Yantar is officially an oceanographic research vessel with underwater rescue capability, but it is also a member of the Russian navy. It is operated by the country’s Main Directorate Deep-Sea Research, which is part of the defence ministry.