The 43-year-old Assange fears extradition to Sweden to face allegations of rape and sexual molestation, which he denies.
At the hearing in the Stockholm District Court, prosecutors demanded that the warrant, issued in late 2010, should be upheld to secure Assange's return to Sweden.
They rejected Assange's suggestion that they question him in London.
"It would involve questioning a number of people a second or third time, among them possibly Mr Assange. To what extent this questioning can be carried out with the help of judicial assistance from our colleagues in Britain is difficult to say," prosecutor Marianne Ny told a press conference.
Assange's defence team, which had maintained that the investigation had been unreasonably long, said it would appeal the ruling.
"The last word hasn't been said yet on this. We will appeal this, and we expect it to change," said Thomas Olsson, a member of Assange's defence team.
The WikiLeaks founder sought refuge with Ecuador in June 2012 after exhausting all legal options in British courts to avoid being extradited to Sweden.
He has said he fears that his being sent to Sweden would be a pretext for his transfer to the United States, where WikiLeaks sparked an uproar with its publication of thousands of secret documents.
Ecuador Foreign Minister Ricardo Patino called the ruling "bad news".
"The government of Ecuador will not abandon its commitment to defend Julian Assange's human rights until he can get to a safe place," he said on Twitter.
Assange supporters who had assembled outside the Ecuadoran embassy in London were disappointed, but some also said they were not surprised.