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."
Despite more than 100 tips from the general public since the alarm was raised, Sweden's armed forces have not located any vessel. Lagersten said the navy would nonetheless remain on high alert and flight restrictions were still in place off the coast of Stockholm in the area of the search operation.
"The intelligence gathering operation is continuing just as before…. We still believe there is underwater activity," he said.
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.
Late Tuesday the armed forces said it was pursuing a further two concrete leads, bringing to five the number of "credible" photos and sightings of suspicious marine activity confirmed by the military in the inner islands of Stockholm's archipelago.
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.