Mr Assange has spent two years at Ecuador’s London embassy to avoid extradition to Sweden over allegations of sexual assault.
At a hearing in Stockholm District Court, prosecutors demanded that the warrant issued in late 2010 should be upheld.
The court agreed Mr Assange should still be pursued.
“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,” Judge Lena Egelin said.
“He should therefore continue to be wanted for arrest in his absence.”
According to Mr Assange’s lawyers the arrest warrant should be repealed because it cannot be enforced while he is in Ecuador’s embassy.
They also say the Swedish prosecutor should have considered the possibility of interviewing Mr Assange in London.
Mr Assange’s defence team is reported as saying they will appeal the decision.
Swedish prosecutors want to question him over sexual assault allegations made by two female former WikiLeaks volunteers.
Mr Assange denies the allegations and has been fighting a legal battle against extradition since his arrest in Britain in 2010.
Mr 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.