It has all the makings of a Cold War thriller – an emergency military deployment with stealth ships and helicopters hunting for a foreign submarine in the Stockholm archipelago. Grainy photographs of a mysterious vessel. Sightings of a black-clad man wading in shallow coastal waters.

Whether it was caused by paranoia or a secret naval mission, Sweden’s biggest military mobilisation since the Cold War over the last three days has underscored growing concerns about Russian President Vladimir Putin’s intentions in the Baltic Sea region.

In just over a month, an Estonian intelligence officer has been reported abducted by Russian forces, Finland has complained of Russian interference with one of its research vessels, and Sweden has lodged an official protest over a “serious violation” when Russian warplanes entered its air space.

Russia has long seen the Baltic as part of its sphere of influence

The maritime mystery has fired the imagination of the region.

Moscow has denied it has any submarine in mechanical trouble in Sweden’s waters, but nervous governments fear that the Baltic Sea could become the next flashpoint with Russia after Ukraine.

Swedish corvette HMS Stockholmpatrolling Jungfrufjarden in the Stockholm archipelago yesterday. Photo: Reuters

“This may become a game-changer for the security in the whole Baltic Sea region,” tweeted Edgars Rinkevics, Latvia’s Foreign Minister, where officials say there has been a marked increase in Russian submarines and ships navigating close to their territorial waters. The search in the Baltic Sea, fewer than 50 kilometres from Stockholm, began on Friday and reawakened memories of the final years of the Cold War, when Sweden repeatedly chased suspected Soviet submarines along its coast with depth charges.

But there have also been many false alarms. In the 1980s, the military on several occasions thought it had detected submarines, only to find the underwater sounds had been made by minks or otters.

The military say they are now looking for a submarine, a mini-submarine or even divers amid the thousands of islands near Stockholm, many of them popular holiday destinations. On Monday a no-fly zone was declared around the search area.

Growing tensions since the Ukraine crisis have already caused Sweden and Finland, both avowedly neutral before joining the EU in 1994, to openly discuss Nato membership. Sweden’s own military questioned its ability to defend itself for more than a week against a Russian attack after Nato warplanes were scrambled last year to meet Russian bombers rehearsing a bomb run on Sweden.

“This kind of incident deepens the sense of insecurity not only in Sweden but also the rest of the Baltic Sea region,” said Anna Wieslander, deputy director at the Swedish Institute of International Affairs.