Healey said the Yantar (Amber) vessel was being "used for gathering intelligence and mapping the UK's critical underwater infrastructure".
"I also wanted President Putin to hear this message: 'We see you, we know what you're doing and we will not shy away from robust action to protect this country'," he told MPs.
The ship entered British waters on Monday about 45 miles (72 kilometres) off the country's coast, with the Royal Navy dispatching two vessels to monitor it, Healy said.
"It was detected loitering over UK critical undersea infrastructure," the defence minister said.
He added the ship was now in the North Sea, "having passed through British waters".
A French official told AFP that French military resources had also been mobilised to monitor Yantar but the ship "had no proven hostile intent".
"It happens regularly that a Russian vessel passes through and there is always close surveillance that is put in place," the official added.
Healy said it was the second time the Yantar had been detected in British waters recently, after it was also spotted in November.
British warships have tracked Russian navy vessels on several occasions in recent months.
Earlier this month, the Royal Navy revealed that in late December the frigate HMS Somerset had tracked a Russian naval group as it sailed from the North Sea to the English Channel, although the group had stayed in international waters.
In September last year, Royal Navy warships spent a week "closely shadowing" four Russian vessels in UK waters, while two Royal Air Force jets scrambled to intercept two Russian aircraft operating near the UK, the navy said in a press release.
The RAF is to provide aircraft for a new NATO deployment designed to strengthen the protection of offshore infrastructure in the Baltic Sea.
It comes after the suspected sabotage of several undersea telecom and power cables in recent months with experts and politicians accusing Russia of orchestrating a hybrid war against the West as the two sides square off over Ukraine.
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