The paper printed a photo of the vessel, which showed it had a number of towers and appeared to display Russian Navy symbols.
A spokesperson for the Swedish military told The Local on Friday that the ship seen in the area had every right to pass through Swedish and Danish waters.
"The ship was involved in a totally normal right of passage," said Marie Tisräter, an information officer for the Swedish Armed Forces.
Jenny Larsson, a spokesperson for the Swedish Coast Guard confirmed the same information to the TT news agency, adding that she accepted that the vessel's actions "may seem provocative".
Sweden's government announced earlier this year that it was set to invest 10.2 billion kronor into its armed forces.
It has also stepped up its exercises with NATO and moved to secure closer military ties with neighboring countries.