"The government does not agree with the assessment made by the majority of the Working Group," the foreign ministry said in a letter to the panel, adding that the body does not have the right to "interfere in an ongoing case handled by a Swedish public authority".
Swedish authorities issued a pan-European warrant in 2010 for his arrest over a rape allegation and was detained in London before being released and later seeking asylum at Ecuador's embassy.
"Mr Assange is free to leave the embassy at any point and Swedish authorities have no control over his decision to stay at the embassy," the Swedish ministry said.
"Mr Assange can therefore not be regarded as being deprived of his liberty due to any decision or action taken by the Swedish authorities."
Assange, who has been holed up at the embassy since June 2012 to avoid arrest, had said he expected British police to call off their attempts to detain him if the panel ruled in his favour.
The 44-year-old Australian fears he could be extradited to the United States be tried over the publication of hundreds of thousands of classified documents by WikiLeaks.