Battleships, minesweepers, helicopters and more than 200 troops have scoured an area about 30 to 60 kilometres (20 to 40 miles) from the Swedish capital since Friday following reports of a "man-made object" in the water.
"Some of the ships have returned to port," armed forces spokesman Erik Lagersten told reporters, adding that it was a "new phase" and not a scaling down of the operation.
"Ground and airforce units as well as some naval units are staying in the area."
"The intelligence gathering operation is continuing just as before.... We still believe there is underwater activity," he said.
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Sweden released a hazy photograph of what might be a mini-sub on Sunday amid widespread media speculation that a Russian oil tanker circulating for a week outside Swedish territorial water was acting as a "mother ship" to the vessel.
Russia has denied it is the source of the suspicious underwater activity, blaming a Dutch submarine for triggering the submarine hunt, a claim rejected by the Netherlands.
The massive military operation has evoked memories of the 1980s for many Swedes who recall dozens of occasions when the Nordic country's navy was in hot pursuit of suspected Russian submarines.
But during more than a decade of Cold War submarine hunts Sweden never succeeded in capturing one, except in 1981 when the U137 ran aground several miles from one of Sweden's largest naval bases, triggering an embarrassing diplomatic stand-off for Russia.