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"This means the bulk of ships and amphibious forces have returned to port," the armed forces said in a statement, adding that some smaller forces would remain in the area.
In what was the country's biggest military mobilisation since the Cold War, more than 200 troops, stealth ships and helicopters scoured waters after reports of foreign "underwater activity" - suspected to be a Russian sub.
Sweden has boosted its military presence in the Stockholm archipelago to search for "foreign underwater activity" in the county's largest mobilisation of troops and ships since the end of the Cold War.
The search in the Baltic Sea less than 31 miles (50 km) from Stockholm began on Friday and this operation comes amid increasing tension with Russia among the Nordic and Baltic states over the Ukraine crisis.
Finland last week accused the Russian navy of interfering with a Finnish environmental research vessel in international waters.
Swedish military spokesmen said the information about suspicious activity came from a trustworthy source and that more than 200 military personnel were involved in the search.
Swedish daily Svenska Dagbladet, citing unidentified sources with knowledge of the search, said the military operation began after a radio transmission in Russian on an emergency frequency was intercepted.
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Sweden is to recognise the state of Palestine in a move that will make it the first major member of the European Union to do so.
The prime minister of the new centre-left government Stefan Lofven said the conflict between Israel and Palestine can only be solved with a "two-state solution".
"Sweden will therefore recognise the state of Palestine," Lofven said during his inaugural address in parliament.
Hungary, Poland and Slovakia recognised Palestine before they joined the EU, making Sweden the first country to acknowledge Palestine while being a member of the bloc.
More than 2,000 people were killed after a seven-week conflict between Israel and Hamas earlier this year.
Swedish scientists are struggling to explain a rise in cases of hypospadias, a condition that causes baby boys to be born with deformed penises.
A 40-year study conducted by researchers at Stockholm's Karolinksa Institute found that incidences of hypospadias in babies born after 1990 jumped significantly from 4.5 boys out of every 1,000 to eight per 1,000.
The scientists said that they had taken into account factors such as low-birth weight that could be linked to the condition, but still could not explain the rise, The Local reported.
Hypospadias means the urethral opening is abnormally placed and can affect urination and sexual function later in life.
Lead researcher Dr Anna Skarin Nordenvall told Dagens Medicin newspaper that an unknown factor could be behind the deformities.
She said that scientists could not rule out the theory that chemicals - specifically environmental agents known as endocrine disruptors - could be responsible for the trend.
Endocrine disruptors, which are mostly man-made, can be found in pesticides, plastics and various household products.
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