Assange says he fears Sweden could in turn extradite him to the United States to be tried for one of the largest leaks of classified information in US history.
"All in all, the district court makes the assessment that the reasons for the arrest warrant offset the infringement and adverse effects the measure entails for Julian Assange," district court judge Lena Egelin said.
"He should therefore continue to be wanted for arrest in his absence."
Assange's lawyers have argued the arrest warrant should be repealed because it cannot be enforced while Assange is in the embassy and the Swedish prosecutor had not considered the possibility of interrogating him in London.
Thomas Olsson, one of Assange's Swedish lawyers, said he would appeal the verdict. Ecuador, which has granted Assange political asylum, wants London to assure him safe passage to Quito. But Britain has surrounded the Ecuadorian embassy with police officers round the clock ready to detain him if he leaves it.
British police say they have spent £6 million ($10.28 million) from June 2012 until March this year on policing costs at the Ecuadorian embassy.
In an interview with Reuters last year, Assange said he would not leave the sanctuary of the embassy in London even if Sweden stops pursuing sexual assault claims against him because he feared arrest on the order of the United States.