The Swedish military launched a major search operation late Friday after sightings of an unidentified vessel around islands off Stockholm.
A Russian defence ministry official suggested earlier Monday that the vessel could be the Dutch Bruinvis, which had taken part in exercises off the coast of Sweden.
"To remove tensions in the waters of the Baltic Sea and to save money of the Swedish taxpayers we would recommend (Sweden) to turn to the naval command of the Netherlands for an explanation," the unnamed official was quoted by Russian news agencies as saying.
But the Dutch defence ministry said its submarine was no longer in the area when the mystery vessel was reportedly sighted.
"We participated in an exercise with Sweden with several ships, but it ended last week Thursday," Dutch defence ministry spokeswoman Marnoes Visser told AFP.
"The Bruinvis then departed for Estonia, where it has been at anchor in the Tallinn harbour over the weekend."
The Bruinvis was now making its way back to the Netherlands, Visser added.
"The Dutch submarine is not involved and we are further not involved in any search action or such," she said.
Swedish Rear-Admiral Anders Grenstad on Sunday said the armed forces were carrying out an intelligence operation to establish the presence of a foreign vessel.
A Swedish media report suggested that a Russian emergency transmission had been intercepted from the vessel — indicating that a Russian U-boat was in trouble in the area. But Grenstad declined to comment on the claim.
IN PICTURES: 'Foreign activity' in Swedish waters