"We have begun an intelligence operation... Involving ships, helicopters and several ground units," Commander Jonas Wikstroem told reporters.
He said the operation was based on a tip-off from a "credible source" and that about 200 Swedish troops were involved. He added that no weapons had been used in the operation.
Wikstroem did not specify how close the operation was to the Swedish capital, nor whether the activity involved one of more submarines, but said that he was informing the public as the area has "heavily trafficked".
In recent months, Sweden has seen an uptick in Baltic Sea manoeuvres by the Russian air force -- including an incident in September when two SU24 fighter-bombers allegedly entered Swedish airspace in what Foreign Minister Carl Bildt called "the most serious aerial incursion by the Russians" in almost a decade.
"As the government has said, the situation has deteriorated in the Baltic Sea," Wikstroem said Friday.
During the Cold War the then-neutral -- and now non-aligned -- Nordic country was regularly on alert following Russian submarine sightings, including one notable case in 1981 when a Soviet U-boat ran aground several miles from one of Sweden's largest naval base.