Speaking at a packed press conference on Friday, Supreme Commander of the Swedish Armed Forces Sverker Göransson revealed that a foreign vessel was in Stockholm's archipelago in October.
But he said the Swedish military had been unable to determine which country it came from.
"We have confirmation that there has been a small submarine in the archipelago," he told reporters.
Prime Minister Stefan Löfven added: "We will defend our territorial integrity using all means at our disposal."
He also announced the creation of a new national security council amid a deteriorating global security situation.
Stefan Löfven took questions from the Swedish media before rushing to a meeting with Albania's Prime Minister. Photo: TT
#Sweden says it has proof there was a foreign submarine in #Stockholm last month but doesn't know where it came from pic.twitter.com/CIYMLR20zu
— Maddy Savage (@maddysavage) November 14, 2014
TIMELINE: Sweden's submarine hunt
Earlier this week an unnamed source speaking to the Svenska Dagbladet newspaper said the Swedish military believed it was "likely" that foreign underwater activity had taken place and classified the case accordingly, in the second most serious category out of a possible six.
"During 10 years of obsessive Cold War submarine hunts, they never came up with anything, nothing at all," he told news agency TT.
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